Codename Phoenix
by SonicH2O
Summary: Shaw storms back into their lives the same way she left, saving them all from a hail of gunfire and certain death. Reese and Finch still refuse to trust her. Shaw doesn't blame them. Root does. Ongoing. Root x Shaw. Post S4 Finale.
1. Fallen

/Location: Hong Kong

22°16'41.2"N 114°10'54.2"E

1435 HKT

6 May 15/

Shaw sighed and ran her hand over her forehead, using her sleeve to wipe away the growing layer of sweat. She grit her teeth, equally frustrated by the heat and by the random sputtering of the dying AC unit in the tiny apartment.

Then there was the whimpering. That was getting annoying.

"Shut up," she said quietly, sending the apartment's actual occupant an icy glare. The man, boy really, was 19; a student at a local university. He got the message, and Shaw watched his throat as he swallowed down any additional noise. He curled himself further into a ball, wrapping his hands over his bent legs as best he could with all his limbs wrapped in duct tape.

Satisfied that he would remain quiet, at least for the time being, Shaw glanced down the scope of her rifle again. She pressed a finger to her ear.

"Lambert, I have eyes on target," Shaw said quietly, leaning forward into her scope. Richard Chow, 58, businessman, entrepreneur, and top money launderer for the Triad, straightened his tie as he stepped out of his car. He was also a father of three with his first grandson on the way, but Shaw knew better than to think about _that_ part.

"Fantastic news Sameen," the British man replied, slightly out of breathe.

"Six men on his security detail," she sighed angrily. "I knew you spooked him last night."

"Well," Lambert grunted, "Humans are hardly perfect now are they dear?" Lambert grunted again, and Shaw heard the sound of a skull hitting concrete. She rolled her eyes.

"You almost done?"

"You show so little concern for your partner. It really is disappointing," Lambert pouted, his breathing steadying.

"I have eyes on the briefcase," Shaw added. Chow's silver Halliburton case was cuffed to his wrist.

"Splendid," Lambert replied, sounding practically giddy. Shaw grit her teeth. "On your mark then."

Shaw sighed and drew in a breath to steady herself. She let it out slowly, lining up her shot. Her finger twitched on the trigger once as a sudden gust of wind burst across the street. It passed, and she fired.

Chow crumbled to the ground and everyone around him on the busy streets started to scream, running for cover. Chow's men pulled their weapons, simple pistols, which didn't possess enough range to even see the barrel of her sniper rifle, let alone allow them to take a shot at her. They went down quickly; a shoulder graze here, a leg there.

"Am I clear Sameen?" Lambert asked, sounding bored.

"Don't call me that," she hissed, lining up another shot. She watched the man fall to the ground, his face twisted in pain. "Five down, no eyes on the sixth." She scanned the area quickly, eyes wide, looking for any sign of movement as her rifle skimmed over cars, trash cans, trees, anything that could provide cover. Shaw found him easily; half hidden behind an industrial dumpster. She moved the scope to his legs, but he fell to the ground before she could pull the trigger. Lambert stepped out from behind the body and Shaw grit her teeth.

"Found him," Lambert looked in her general direction and smiled as he tucked his silenced pistol back into his coat. Then he strode purposefully towards Chows dead body, quickly picking the lock on the briefcase.

"Got it."

"You didn't have to do that," Shaw said finally.

"As adorable as it is that you still insist on knee capping everyone we meet, we're on a deadline," Lambert said coolly.

"He wasn't our target."

Lambert sighed. "I suggest you get out of there before the police arrive."

Shaw nodded numbly in agreement, pulling the rifle back from the window.

"And Sameen…" Shaw froze. "Samaritan gave no further instructions on what was to be done with that boy. So tidy up as you see fit."

Shaw let out a breath she hadn't realized she was holding and closed her eyes for a moment. She pivoted quickly, grabbing a knife from the kitchen. The boy started to whimper and cry, and Shaw knew if there wasn't duct tape over his mouth he'd be begging for his life. She stabbed the knife viciously into the back of the chair she had occupied and turned to him. Then she squatted down in front of him and grabbed his collar, pulling him closer.

"You can play this one of two ways. One, you can wait till I'm gone and try to cut yourself free. The cops will be here in two minutes and eight seconds. You won't be done by then. And I don't think you really want to explain what you're doing with a GM6 Lynx on your kitchen table. Especially not one that was just involved with a double homicide, so I'm going to suggest you take door number two, and just sit there quietly for the next 97 seconds until the police arrive," Shaw's face contorted into a bitter, menacing smile. "Sound good?" The boy nodded furiously and she released his collar, letting him fall back against the wall as she headed for the door.

Shaw ducked into the hallway with nothing but a silenced pistol tucked into the waistband of her black jeans. She strolled casually to the end of the hall before sliding into the side stairwell. Shaw took them two at a time, bounding out into a back alley where Lambert was already waiting for her in their car.

"You look positively dreadful," Lambert smirked, taking in her sweaty appearance as she entered.

"It's the heat," she muttered angrily as Lambert shifted the car into drive.

"Well no wonder, with the way you're dressed," he gestured to black jeans and long black sleeved shirt she wore.

Shaw's jaw clenched. "When I wear short sleeves people tend to stare," she sneered.

Lambert grinned back at her, unfazed by the menacing glare in her eyes. "To be fair, I did ask nicely first," he reminded her, clearly enjoying the way her jaw clenched and she went deathly still.

"What's next?" she asked finally, shifting uncomfortably in her seat.

"Passports in the glove compartment," Lambert nodded towards it, "With the tickets."

Shaw leaned forward, wedging the compartment open to find a manila folder. She dumped the contents onto her lap. Sameen Drake, from Nevada, a pharmaceutical sales rep returning to the states from a business trip abroad. Her eyes widened as she picked up the tickets.

"Is this a joke?"

Lambert pretended to pout when he looked over at her, "And here I thought you'd be so excited to be going home Sameen."

Shaw stared at the ticket intensely, not quite sure what game Greer, Samaritan, Lambert, whoever was playing. She was holding a one way ticket to JFK airport.

"Don't call me that," Shaw grumbled. Lambert just smiled, returning his eyes to the road as two police cars raced past them.

/Location: New York: Below Ground

40°42'50.1"N 73°59'53.9"W

0300 EDT

7 May 15/

The sound of a phone ringing made Root bolt upright. Her eyes were blurry and there was a burning in her side that made her wince, but her hand was already wrapped around her gun before another hand covered hers. Harold's.

"It's ok Ms. Groves," he soothed, before returning his attention to his computer station.

Nodding once, Root let her heart rate settle, moving her hair from her eyes as she felt her breathing normalize. "Why didn't you wake me?" She asked, her voice hoarse.

Harold's eyes darted to her briefly, contemplating his answer. "Mr. Reese was perfectly capable of taking first watch," he said evenly, his lips pursed into a thin line. "With your injuries-"

"We both got shot Harold," Root sighed, still feeling too tired to argue the point. Her eyes drifted to John. He had his back to them and he was whispering into his phone. If they had been followed, if Samaritan was going to storm their little headquarters, it probably would have happened already. Standing watch was probably an unnecessary precaution. But with The Machine gone they had no way of knowing for sure.

"Yes," Finch's eyes followed her line of sight to Reese, his shoulders hunched, blood stains still evident on his black jacket, "I'm sure Mr. Reese will appreciate the rest, if you're feeling more awake," he conceded.

"Doesn't matter now Finch," Reese said evenly, his face unusually grim. "I have to go." He tucked his phone into his pocket.

"Mr. Reese, this is not the time to-"

"That was Fusco, on the phone. A sniper killed Dominic and took a shot at Elias," Reese explained quietly.

"Took a shot on Elias?" Root questioned, cocking her head to the side as she considered all the possible implications.

"Through and through to the shoulder. High powered rifle. Did a lot of damage," Reese's lips were pressed into a thin line that almost exactly mimicked Harold's, and not for the first time Root found herself wondering which one had picked up that particular quirk from the other.

"But Mr. Elias is alive?"

"Just. Fusco has him in the hospital under a fake name, but that won't hold," Reese sighed.

"As much as it pains me to suggest this, is it even wise for you to go back to work?" Harold asked, his eyes darting to her.

Root sighed, a bitter smile pulling at the corner of her lips. "I don't know," she admitted quietly. "The blind spot The Machine installed in Samaritan should keep Detective Riley and Professor Whistler's covers in place, but…" she shrugged.

"And what about your cover Ms. Groves?"

"I don't think I have one Harry," her smile widened, revealing her teeth, but she could feel her eyes water and quickly let it slide off her face. The Machine had created new covers for her almost daily. Her last cover, Abbigail Burkle, was a bartender in the West Village, but she'd had that identity for mere days before The Machine had been pulled offline. If anyone so much as looked at that cover funny it would collapse on itself.

"Either way Finch," Reese sighed, "We need to get Elias somewhere safe."

Root's eyes widened, "Are you suggesting we bring him here?"

Reese's shoulders tensed. "No…that would be bad," he acknowledged quietly. "But if someone is trying to start a street war, killing the head of the Brotherhood and taking out Elias is a pretty good way to start."

"Someone?" Root scoffed. "It's Samaritan."

Harold's frown deepened. "Why would Samaritan kill the heads of both organized crime syndicates? That only leads to instability."

"Unless Samaritan is making a play," Reese offered, his brow knitting together in concern, "Samaritan already has the governor of New York in his pocket, why not the head of a new crime family?"

Root nodded thoughtfully. "Even Samaritan can't figure out how to stop organized crime. But controlling it? That's doable. And terrifying."

"Yes. Completely," Harold murmured thoughtfully. "But who is Samaritan's heir apparent?"

"A good question," Reese nodded, "One I hope you two can figure out while I get Elias somewhere safe."

"The safehouse in Tribeca should be…uncompromised," Harold offered. Reese nodded as he moved back to the lockers, switching his blood covered dress shirt for a clean one. He did it slowly, but still couldn't stop a grimace from crossing his face. Root winced as she watched him switch shirts, knowing she'd be making a similar face soon, just as soon as she felt confident she could make it to her feet without collapsing.

Harold's eyes snapped back to her when Reese left and she was sure he could tell how tightly her jaw was clenched. "You can sleep Ms. Groves," he assured her quietly.

Root shook her head quickly, regretting it instantly as another wave of dizziness hit her. "No, I'm fine," she assured him, her eyes drifting past him to the black briefcase open on the counter. "How is She?" she asked, her voice trembling.

"I'll need more time to know for sure but…She…" Harold hesitated as he stumbled over the pronoun, suddenly unable to meet Root's gaze, "recognized Mr. Reese and myself. And asked if you were alright Ms. Groves."

Root managed a small smile, relief flooding through her. "So She's intact?"

"There is still a nearly infinite amount of code to sort through and tests to run before I could truly make any statements about our success. But yes, I am…optimistic about the results," Harold said evenly.

She leaned her head back against the side of the car, her eyes fluttering closed despite her best efforts. "Optimism Harry?" she teased, her voice unsteady.

Harold smiled softly back at her. "Just rest Ms. Groves, we're safe here," he promised.

"Is anywhere safe anymore Harold?" she murmured softly, feeling her eyelids grow heavier.

* * *

 _Hopefully there is some interest for me to continue. Thank you for reading! 11/08/15_


	2. New Streets

_Glad there was some interest!_

* * *

/Location: New York: Below Ground

40°42'50.1"N 73°59'53.9"W

2300 EDT

10 May 15/

"My money's still on the Triad," Reese sighed.

Root bit her lip and returned her attention to the side of the train, which was covered in information on the Triad and the Russian mob. There were old photos of grizzly murders both had caused, newspaper clippings, and their new surveillance photos. The photos included Victor Tang, the Triads young leader, outside one of their many meth labs, and Alexi Ansmiov, the former FSB agent who led the Russians outside one of his illegal gambling parlors.

"We are not betting on the outcome of a New York street war," Harold retorted, clearly appalled.

Root felt the hint of a smile on her face. Shaw would've taken that bet. "It's the Russians," Root said calmly.

She stared at the messy collage she and Reese had cobbled together. Trying to survey the two strongest gangs left in New York with just two people (while also avoiding all cameras) was proving nearly impossible and completely exhausting.

"So, what, 20 bucks?" Reese deadpanned, his lip curling into the slightest hint of a smile.

Root felt her own smile grow, "I don't make enough money to take that bet John," she reminded him.

"This is not happening," Harold scolded, his head turning nervously between the two of them.

"You're a bartender, shouldn't your tips-"

"Barely cover my overpriced apartment, I can do ten," Root countered.

Reese nodded while Harold seethed quietly.

"Well, whoever Samaritan has chosen to back in this fight will be…formidable," Harold said tightly, clearly hoping to change the topic. "Mr. Tang is young and eager to prove himself. He slaughtered his way to the top of the Triad leadership in a coup, essentially. And Alexi's work for the FSB was sealed. It took hours to crack the encryption…and quite frankly I wish I hadn't," He shuddered. "These pictures Ms. Groves took of the Triad's facilities seem to indicate that they are more than capable of supplying this cities heroin while the Brotherhood is in disarray," he sighed. "However, the sheer volume of guns the Russians are trafficking is staggering."

"Are those anti-aircraft missiles?" Root asked, pulling one of the pictures off the wall.

"I believe that is precisely what they are Ms. Groves," Harold nodded grimly.

"Most of the arms Alexi's crew are trafficking are meant for destabilized regions, selling to various terrorist groups, rebellions, whoever wants it," Reese explained.

"Whoever wants it and can pay exorbitantly," Harold added.

Reese nodded slowly, "So, it's a coin toss. Triad controls the drug trade and the Russians controls guns."

"Perhaps... On the 6th, one Richard Chow was killed in Hong Kong by a sniper," Harold explained, pinning a news clipping to the train car, "While he was never charged, authorities had long suspected him of being one of the Triads top money men. No doubt his death was just another part of Samaritans May 6th Massacre."

"I'm glad I didn't bet a twenty then," Reese muttered.

"It's possible this indicates Samaritan is backing the Russians, yes. However it could simply mean Chow refused to cooperate in some manner," Harold mused. "We don't have enough information to reach any conclusions."

Roots gaze drifted back to John and he looked at her grimly. She sighed, exhausted. This would kill them. Fighting this battle would be their last pitiful stand against Samaritan. They were children sticking their fingers in a leaking damn. "What's our long term plan here Harry? We take out one crime ring and…what?"

Harold sank into his desk chair, "Truthfully…I don't know Ms. Groves. But we cannot let Samaritan control both our elected officials and the criminal underworld."

"We need Her. What can we do to-"

"The Machine is hanging on by a thread Ms. Groves, in absolutely no shape to be thrown back out against Samaritan," he huffed.

"I know that She isn't ready, but we need to make Her ready," Root argued. "I talked to Her earlier," Root sighed. "She said She gave you locations, possible places to hide Her, once She's up. We should look into them."

Harold stayed quiet a long moment, looking at his feet. His head snapped up suddenly, "The Machine already lost to Samaritan once. Unless we find some way to substantially alter the odds…the best thing for The Machine right now is to be here. Safe," his large eyes bore straight through her until he was convinced the argument was over and then he nodded once, pivoting back to his computer.

"We need Elias," Reese said quietly. "He still has support in the city. Money, weapons…soldiers. If he makes a play people will pay attention."

"He is the devil we know," Harold agreed wryly.

"Can he win?"

"He can give us time," Reese sighed. "I'll ask him. I have to head over to the safehouse to relieve Fusco anyway."

Root gestured to her shirt collar, "You have something…" She grimaced as she realized why he was bleeding. He'd popped his stitches.

He glanced down, rolling his eyes at the small pool of blood staining his collar. "Not again," he muttered, turning to rummage through the lockers for a clean shirt.

"I do wish you would take your present condition into consideration Mr. Reese," Harold mused, masking his concern behind his scolding tone. "And not pop your stitches for a fifth time," he added under his breathe.

"I'll be fine Finch," Reese winced as he changed, undermining his words entirely.

"And I guess I'll go take some more pictures of the Russians," Root smiled bitterly as she grabbed the camera from the counter.

"Wouldn't it be better for you to get some rest Ms. Groves?" Harold called after her.

"Crime doesn't sleep Harry," she smirked at him, cocking her head teasingly. She turned to leave.

/Location: New York

40°32'17.8"N 74°07'50.3"W

0200 EDT

11 May 15/

Root shoved her seat back, kicking at the floor of the car to give herself extra room. Squirming until she found a comfortable position, she settled in, sipping slowly from the thermos of coffee stowed in the cup holder.

Whatever shipment the Russians were hanging around the docks waiting for seemed to have arrived. The five men at the dock perked up, guns at the ready. Root felt anxiety bubbling in her chest. This was typically the part where She whispered something in her ear. Nothing significant, just some clue so Root wasn't flying blind. She steadied her camera on the dashboard just as a pair of headlights pulled around the corner. Root squinted against the light, blinking rapidly to adjust. The headlights belonged to a small cargo truck. Two men jumped out of the cab, the driver, a squinty eyed man with a half-grown beard and Alexi Ansimov.

Root adjusted the angle of the camera slightly, hoping to get some decent shots of Alexi. Root cocked her head as she watched him. He was, by all standards, incredibly average; almost 40, just under 6 feet tall, neither immediately imposing nor non-threatening in size. While his goons were all wearing jeans and leather jackets Alexi was dressed more elegantly, in a sport coat and a baby blue button up. Root frowned. Why dress business casual for moving cargo?

"Well hello lovely," Root turned, her gun halfway out of her pocket, but it was too late. Lambert grinned at her cheerfully, a silenced pistol pointed right at her from outside the passenger side of the car. Keeping the gun trained on her, Lambert opened the passenger side door and slid in. "I must say, this is such a fun reversal of our last conversation," he teased. He opened the glove compartment. "Guns," he gestured to her with his free hand. She reached behind her, pulling her pistol from behind her back. "The other one too Ms. Groves," he smirked.

Root bit down a growl, flashing him a large smile as she handed it over. He stuffed them into the glove compartment and closed it. "I like the redecorating you did," she gestured to the left side of his face, where a large burn almost an inch thick ran from the tip of his jaw to just below his eye. Lambert smashed the camera against the dashboard, scattering pieces of it everywhere.

His grin widened. "I thought you might. Your little girlfriend gave that to me actually. At the Stock Exchange," Roots eyes widened and she hated herself for giving anything away. "But not to worry," his grin widened, "I got her back."

Roots hands curled into fists at her side and she had to remind herself to breathe. "Where-"

"You know I won't tell you that lovely," he chided, his voice full of more condescension than Root had ever heard in her life. Her fingers dug into her palms deeper, drawing blood. If Shaw was alive, getting herself shot here wouldn't do her any good, she ran the words through her head over and over. He stared at her for a long moment, his thumb tapping against the back of his gun.

"Well, we can stop guessing who Samaritan is backing now," Root said quietly.

Lambert kept grinning. "I do suppose my presences tips our hand slightly," he shrugged. "I could kill you."

"You could try," Root sneered and Lambert laughed.

"I've heard Sameen make many similar threats," he mused.

"Don't call her that," Root snapped, feeling her throat begin to close. She swallowed hard, fighting back tears that were so much closer to the surface than they had any right to be.

Lambert cocked his head slightly, and the left side of his mouth twitched slightly in amusement, "You know she gave you up right lovely? Baited you to a psychiatric facility to be lobotomized, all that?"

"You're lying," Root hissed. They'd fed her that line before, it wasn't true. It couldn't be.

Lamberts grin faltered, something close to pity crossed his face, "You really believe that. That we could have Sameen for nearly a year and she wouldn't break. That she'd just…take it," he shook his head.

Root lunged for him, one hand reaching for the gun, pushing it away from her while she used her other to claw at the wounded side of his face. Everything around her seemed to fade from existence, she just wanted to do as much damage to Lambert, to his cocky smile, as humanly possible. He screamed in pain as her fingers dug into the sensitive skin by his burn and he grabbed furiously at her wrist, twisting it until Root heard a snap and felt a wave of pain flash through her. Lambert abandoned her injured wrist, punching her squarely on the jaw, rocking Root back against her chair, blinking back stars that swam across her vision.

Lambert chuckled humorlessly as he pointed the gun at her again. With his free hand he padded his tie against the deep claw marks she left on his face, leaving his tie speckled with blood. "I liked this tie," he pouted and Root managed to roll her eyes without passing out.

"What do you want," she glared at him defiantly.

"What I always want," he sighed, "World Peace, a Beatles reunion tour, a new tie now." He smirked, "I'm come bearing a message Ms. Groves. The Machine is gone. You can accept that you lost and go on living a relatively normal life under Samaritans protection. Or you can keep fighting the inevitable and die." Lambert's grin widened as his eyes openly surveyed her body, "I do hope you can see how generous that offer is." Root stared at him silently, not trusting her voice. Lambert chuckled. "Well then, I have other urgent matters to attend to," he kept his gun trained on her as he opened the door and slid out. "If I see you again lovely…well, you understand how this works I think?" he smiled and pocketed his gun before heading back down the dock to the Russians.

Root moved her uninjured wrist to her ear. "You get all that Harry?"

"Every word. Are you alright Ms. Groves?" Harold responded, clearly distressed.

She rubbed her wrist gingerly, knowing it should hurt more than it did. But for the first time in weeks she felt a glimmer of hope and that was enough to dull the pain, "Shaw's still alive." She hadn't been sure, after the psychiatric facility, what they would do to her. She hadn't let herself think about it.

Harold's confusion was evident in his silence, "I don't quite understand Ms. Groves…" he said finally.

"He wanted to hurt me. If she was dead…" her voice waivered, "He'd want me to know."

Harold was silent a long moment, "I see," he said quietly and Root bit her lip to avoid screaming at him. In all this time, he had never believed they had a chance to get Shaw back. "They think The Machine has been destroyed," he added, clearly wanting to change the subject. Across the pier, the truck Alexi arrived in backed up and left the yard.

She nodded, still not trusting her voice, until she remembered he couldn't see that. "Small victories," she murmured.

"Indeed," he agreed sighing heavily. "It would probably be best if you left before Mr. Lambert returned," he suggested. Right. Moving. Before that asshole used her deaf ear to get the jump on her again. She grit her teeth. She'd positioned herself to avoid the cameras and to get the shot. She was too used to knowing implicitly and without doubt that The Machine would warn her of danger; a low hum, increasing in decibel as the danger drew closer. Now, it was just silence.

"We might have another problem Finch," Reese's voice suddenly burst in her ear.

"I take it your conversation with Mr. Elias was not a success?"

"Not really," Reese's voice was tight, he was gritting his teeth, Root was sure of it, "He wants to make a deal."

"A deal for what Mr. Reese?"

"His life. And his accountants," Reese sighed.

"What?" Root scrunched her face in confusion as she pulled her car away from the Russians deal, heading towards the ports exit.

"He wants us to escort him and Bruce safely out of the city and he'll give us everything," Reese explained.

"Define everything?" Root asked, frowning.

"Elias has a few Cayman accounts he wants to keep, but everything else, his weapons, his suppliers, his war chest, it's ours. To do with as we see fit," Reese explained.

"Having access to Elias's resources would certainly alleviate some of the financial strain of fighting a rogue artificial superintelligence," Harold conceded.

"The guns would be nice," Reese muttered.

"Maybe," Root agreed, "Still leaves us fighting a Russian army."

"And I suspect that even if we were to get Elias out of the city, Samaritan might not simply let a potential threat go quietly into the night," Harold sighed.

"Probably not."

"Definitely not," Root corrected.

"I explained that to him Finch. All he wants is for us to get him past the city limits," Reese explained. "He didn't seem concerned when I told him I didn't think that would be enough."

"Of course not, he doesn't actually know what he's up against," Root scoffed.

"I must say, I'm surprised that Mr. Elias would opt for flight after all this time," Harold mused.

"He isn't doing it for himself. After he lost Anthony…Bruce is his family. He's worried," Reese said grimly.

"Rightfully so, I'm afraid," Root could hear the wariness in Harold's voice and wondered suddenly when it was he had last slept.

"We should do it," Root declared. "Maybe it's not what we asked for, but its…something."

"Agreed," Reese said heavily.

"I am…inclined…to agree," Harold said slowly, "However, with our identities so precarious…doing this would put us squarely in Samaritans crosshairs."

"What if Fusco took him? Used the shadow map?" Reese asked.

"It would look significantly less suspicious, but I hesitate to put the detective in a position that precarious without backup," Harold admitted.

"Lionel can handle himself Finch," Reese assured him.

"I am certainly not questioning the detective's capabilities Mr. Reese," Harold assured. "Oh-" Harold said suddenly.

"What is it?"

"I believe Mr. Lambert was quite serious when he said he had other plans Ms. Groves. I'm receiving multiple reports coming in of shots fired, not far from your location. Reports that put both the Triad and the Russian mob on the scene."

"Why? What's changed," Reese questioned.

"It seems the Triad attempted to…acquire…the Russians latest gun shipment while it was in transit," Harold explained.

"That's gutsy," Reese said, clearly impressed.

"Yes, and foolish. Especially now that we know they are fighting the Russian mob and Samaritan," Harold sighed.

"Send me the address," Root ordered, pulling her guns from the glove compartment.

"Ms. Groves, with your injuries-"

"Don't Harold," she warned him through gritted teeth. The address appeared in her phone.

"Please, at least wait for Mr. Reese to arrive," Harold protested.

"I'm ten minutes out Root," Reese assured her.

Root slammed on the brakes as she rounded the corner to the address. The truck she had seen at the docks was in the middle of the street, on its side, flames bursting out of it. Gunfire erupted all around her and she slammed the car into reverse to give herself room to assess the situation.

"Then drive faster John," Root said quietly.

* * *

 _Thank you for reading! 11/11/15_


	3. Invisible Hand

/Location: New York

40°41'57.2"N 73°58'48.4"W

0330 EDT

11 May 15/

Root exited her car, staying crouched behind it for cover. From her position, she could make out at least six distinct muzzle flashes coming from inside the impound lot across the street, and above her, in a condemned apartment complex, gunfire was coming from seven or eight different windows. The smoke from the burning truck made the entire street hazy, but down the street Root saw another car pull up. Five more members of the Triad jumped out, shooting haphazardly towards the apartment complex as they moved for cover inside the impound lot. Roots eyes fell back on the truck, the fire was dangerously close to the cab now.

"John, the Russians have the high ground here. I'm not so sure they were ambushed," Root said quietly.

The cabs explosion shook the street, shooting debris out in every direction. Root glanced at the truck again, the blast had blown the back door of the truck wide open. It was empty. Everything suddenly clicked together.

"What are you saying Ms. Groves?"

"The truck is empty. There was no massive arms deal tonight," she whispered.

"Oh dear," Harold's voice rose an octave, "Ms. Groves, you must get out of there."

"No Harry, if the Russians planned this it was to draw out Triad leadership," Root argued. "If this succeeds, then they will be virtually unchallenged across the city."

"I understand the implications, however you cannot singlehandedly stop a war Ms. Groves," he pled.

Roots eyes scanned up and down the block until she found what she needed; a door to the apartment complex was ripped off its hinges, giving her an easy entry point. "I don't need to. I just need to give the Triad room to retreat. I can get inside the building the Russians are using for cover, clear it out…maybe take out Alexi…if he's here," Root explained.

"Ms. Groves, if you insist on this approach, then please, wait for Mr. Reese," Harold argued.

"I'm two minutes out Root," John added.

There were screams coming from the impound lot and Root sighed. "I don't think they have two minutes Harold."

"Please Samantha-do not risk your life in this fight," he begged.

Root smiled, touched by his concern, even if his use of her first name infuriated her. She moved quietly towards the unguarded stairwell.

"If you won't listen to me…" Harold's voice was becoming more desperate. He sighed suddenly, guiltily, "Then do it for Sameen."

Root froze, blood rushing to her ears. How dare he-

"If you believe she is still alive, that Mr. Lambert's words confirm that, then dying tonight will accomplish nothing," His voice was sterner then she'd ever heard. "Wait for Mr. Reese. Please…For her sake, if not your own," he finished quietly.

Root nodded mutely. "If you ever…" her breathing was erratic, her heart felt like it was about to burst out of her chest, "If you ever use her like that again-"

"I hope I never have to Ms. Groves," Harold said quietly, almost sounding apologetic. "Now please, find cover."

Seething, Root slunk into the shadows and listened to the exchange of gunfire and the occasional screams until John was at her side, an assault rifle in hand, a second hanging around his chest from a strap. "Want one?"

She smiled bitterly, gesturing to her injured wrist. "Probably best I don't," she muttered. Reese nodded.

"Stay behind me then," he said darkly. He pulled a ski mask over his face and handed one to Root.

They cleared the abandoned apartment building level by level, their own gunfire drowned out by the chaos of the firefight.

"Finch, why are there no sirens?" Reese asked as they rounded the stairwell to the fourth floor.

"I believe Samaritan is…rerouting…all emergency calls," he said gravely.

By the time they reached the fifth floor the gunfire was fading, but there was still no sign of Alexi – or Lambert.

They cleared the floor apartment by apartment, until they were at the corner room. The sound of gunfire and muffled Russian voices drifted into the hall. Reese held up a hand, holding Root back. He stealthily crossed to the other side of the door before nodding to Root. Silently she opened the door. The two men in the living room didn't even hear them enter before they were down, groaning in pain from the shoulder and knee shots Reese inflicted. Alerted by the sound of falling bodies, two more lunged out of the kitchen. One swiped at Reese wildly with a knife, cutting right through Reese's coat. Staggering back, Reese fired, only to hear the click of an empty cartridge. He charged the man, slamming him with the butt of his rifle. The Russian wasn't deterred, dragging Reese to the ground with him. The second man moved to jump into the fray.

"Ah, I wouldn't," Root pressed the gun against the back of his skull. "Drop it," she whispered, gesturing to the gun in his hand. He did. "Good," she cooed, quickly aiming her gun to his knee. The man dropped with a scream.

Reese staggered to his feet, giving the man on the ground another kick for good measure.

Shots rang out around them, and they ducked for cover in the tiny kitchen as bullets riddled the walls.

"That's not coming from the impound lot," Reese muttered, poking his head out. He pulled it back quickly. "Two more down the hall." He winced, pressing his hand against his shoulder.

"John?" Root swore softly as Reese pulled his hand back from his shoulder. It was covered in blood.

"Its ok, I just ripped my stitches…again," he smiled tightly. He grimaced and adjusted the strap of the assault rifle on his shoulder.

The two men down the hall continued to fire blindly into the kitchen, splintering the walls and shattering the lights. The room went dark.

"Any suggestions Finch?"

"I'm working on it Mr. Reese," Harold's voice was tight and desperate. Root inhaled deeply, willing herself to be calm. He didn't have an escape plan for them. They would just have to improvise.

Suddenly, four men stormed the apartment. Two rushed the kitchen and Root dropped them before they could raise their guns. Root bit back a laugh. Instead of escaping the Triad had used their distraction to push in on Alexi and the apartment complex. Root sighed. Criminals could never do anything right. She peaked her head around the corner to see the two Russians dead in the hallway, pools of blood around them.

Barely breathing, Root walked forward cautiously, gun raised. She took the first corner, and turned to see the bathroom. It was clear, and she turned back to the hallway. She cleared the side bedroom, feeling her heartrate increase again. She pivoted back to the hallway, where the final door was closed. Standing in the doorway to the side bedroom, she put her hand on the door knob to the master bedroom, waiting for Johns signal. He raised his rifle and nodded. Root whipped the door open just as the two men inside began to shoot wildly in their direction.

Reese grunted in pain and fell back to cover. "Got one," he confirmed. A large red spot began to spread across his arm.

Root waited, not breathing, until she heard the telltale click of an empty clip. She shot through the door as the last man charged her angrily. The man grabbed for her gun, forcing it towards the ground. He struggled against her for a better grip on it, forcing his finger over the trigger. Three shots rang out and Root yelped in pain as she felt one bullet graze down her calf. With the clip gone, the man let go, stepping back to take a swing at her. Root slammed the butt of her pistol against his forehead and he staggered into the wall. Not trusting her weight to her left foot, Root spun the pistol in her good hand, holding the barrel like brass knuckles.

He swung wildly and Root swayed to the side to avoid him, striking him as hard as she could in the stomach. He groaned but didn't stop, charging at her again with his hands outstretched, reaching for her throat. Root tried to lunge out of his way, shifting her weight to her injured leg, but it gave out and she slipped to the ground in a small pool of her own blood. The man slammed against the window and Root turned, ready for his next attack.

She froze.

The red glint of a sniper's laser sight was trained through the window, right on her. Her head started spinning, the sound of her blood pounding into her brain totally overwhelming her ability to move or even breathe. Her lip twitched, and Root didn't know if she wanted to laugh or cry. This wasn't how she thought it would end.

Instead, the man in front of her dropped, his blood splattering across her face. She screamed. Suddenly, Reese charged into the room, grabbing her by the arm, and dragged her out.

"You ok?" he asked through gritted teeth, clearly in considerable pain himself. She nodded numbly, and they hobbled down the stairs together, neither able to fully support their own weight.

When they got to the ground floor they burst through the nearest exit and froze. Four men, all Triad, spun on them, pulling their weapons.

There was a muffled bang and one dropped dead in front of them. The remaining men screamed and wheeled around, towards the impound lot and the sound of the gunfire. Their cries were cut short as each one of them dropped dead moments later.

Root stared at them, wide eyed. Who the hell was that? Reese didn't seem to care, he was half dragging, half carrying her down the block, towards their car.

He threw her into the drivers seat before collapsing in the back. "We need to move Root," he said, his voice low and weak from blood loss.

She nodded, gunning the car in reverse, away from the still smoking truck and the echo of sniper fire.

/Location: New York: Clearwater Impound Lot

40°41'57.2"N 73°58'48.4"W

0839 EDT

11 May 15/

Root tried hard not to limp as she approached the yellow crime scene tape. She adjusted the blonde wig she was wearing and pushed the glasses up her nose. Using a fake identity here wouldn't do much against Samaritan, but her credentials would be good enough to get her close to John and Detective Fusco who were working the case.

She flashed her FBI badge and ducked under the tape. She winced as she took in the damage. There were no bodies left, just bullet casings, chalk outlines, and blood everywhere.

"Augusta King, FBI, I need a status report," she said formally, acutely aware of the many people around them. John waved them off, leaving Fusco and himself to brief her.

"No offense Psycho Barbie, but you really shouldn't be here," Fusco scoffed.

She smiled tightly, ignoring him. "How many?"

"Twenty some injured, two were civilians. Sixteen dead in total. Including all of the top Triad leadership-" Reese explained. Root closed her eyes, a bitter smile creeping onto her face. All of it had been for nothing. "All but one were taken out by the sniper," he finished.

"Anything on our lone gunmen?" she asked John quietly.

He gestured for her to follow him. He walked slowly, barely hiding his own wounds. They stopped at the base of a crane and Reese nodded upwards.

"Snipers nest was intact when we got here."

"In the crane?" Root frowned. That was…so exposed.

John nodded. "High power rifle, a GM6 Lynx equipped with a thermal scope and one hell of a silencer. There was a piece of cardboard laid out across the beams and a black sleeping bag on top of it, sniper crawled up here after dark and was completely invisible other than that red dot from his scope."

"Wait…This doesn't even make sense. The Russians put a sniper up here, behind the Triad?" Fusco scoffed.

Reese shrugged and then winced. "Looks like. The Triad start seeing their guys drop from behind, they try and push up, right into the Russians main line of fire."

Root shook her head, "Carefully orchestrated, lacking all subtlety. This seems to match Alexi's MO," she sighed, "It still doesn't explain the sniper…why didn't he shoot us?"

"I'm not sure. It doesn't add up," he sighed.

Fusco scoffed. "Yeah, you're telling me," he muttered.

"What if it wasn't a sniper for the Russians?" Reese said slowly.

"Then who?"

"I don't know…a third party."

Root felt her mouth run dry. They did not need any more players in this. "Control," she said simply.

"Possibly." Reese hesitated, "Shaw liked the Lynx."

Root nodded, letting her eyes drift along the ground.

"As far as sniper rifles go, it's almost standard issue for the ISA."

"Makes sense then," Root muttered, fisting her hands into her coat pockets to avoid the morning cold.

"You have a funny idea of sense Coco Puffs," Fusco huffed.

"But why would the ISA be here at all?" Root pushed her wig out of her eyes, feeling increasingly frustrated.

"Perhaps," Harold's voice cackled through their earpieces, "Our…talk with Control did some good after all?"

"Not likely Finch. Control considers herself a patriot. She wouldn't even listen when we suggested Samaritan had tampered with the stock market," Reese murmured.

"And after that meeting, I'd think she'd want us dead more than anyone," Root cocked her head, "Well, me at least," she admitted with a small smile.

"Either way, if there are unknown parties, dangerous parties, at play here, we should be very careful. I think it would be best if we got Mr. Elias out of the city sooner than later," Harold said evenly.

"Agreed," Reese sighed.

Root nodded numbly, watching her breathe in the air as she exhaled.

"I'll get it done tonight," Fusco promised.

* * *

 _I know nobody likes not knowing, so Shaw is for sure in the next chap :) Thanks for reading! 11/13/15_


	4. The Good Soldier

/Location: New York

40°41'57.2"N 73°58'48.4"W

0400 EDT

11 MAY 15/

Shaw's finger twitched on the trigger and she felt her heart stop. Even through a thermal scope, the leather jacket, the long hair, and even longer, bony limbs were instantly recognizable. She stared down the scope, completely paralyzed as another familiar silhouette swooped in, dragging Root out of her line of vision. Shaw tried to swallow but couldn't. She pulled back from her rifle, pushing herself onto her elbows, suddenly unable to breathe. She gasped raggedly, struggling to get air to go into her lungs.

It wasn't possible.

Her hands balled into fists, sinking into the black sleeping bag she was hiding in. The wind whipped around the crane, drowning out and distorting the yelling and screaming below her. Even if it was possible, it didn't matter. It couldn't change anything. It couldn't change her mission. She inhaled shakily, moving back to her scope. Four more Triad guys were waiting near the entrance of the apartment building. She breathed deeply.

But it _wasn't_ possible.

They burst out of the front door then, right in front of the four Triad members. They stood there, completely still, staring at the Triad while the Triad stared at them. Shaw rolled her eyes. No, they were definitely real. And making her job overly complicated. She dropped the Triad members quickly, then kept her scope trained on the two of them until they were in a car and retreating. If their slow speed was any indication they'd been injured. Badly.

She moved her scope back down towards the impound lot, picking off the last of the men she'd been brought there to kill. Then she carefully extracted herself from the sleeping bag, climbed down the crane, and ducked out of the impound lot. Sirens wailed in the distance, drawing closer. Samaritan had finally stopped rerouting the emergency calls.

Pulling her hood up over her eyes, she slid into an alley just as a police car streaked by. She pulled out her phone, willing her hands to stop shaking as she dialed.

"Hello?"

"What. The. Hell. Greer," she hissed. She closed her eyes, instantly regretting using that tone.

She could hear his smirk through the phone. "I assume this has to do with Mr. Reese and Ms. Groves rather…unexpected appearance," he said evenly.

Her nostrils flared and she forced the fury boiling in her stomach to stay still, "Yes," she replied, her voice strained.

"And are they taken care of?"

Shaw's jaw felt stuck together, her chest tight. "They weren't my target," she justified, regretting her words instantly. Greer would make them her target. In a heartbeat. She winced. That couldn't happen. "And because my bullets don't work on ghosts," she tried to stop the rage that was flowing through her, making it hard to see, "And seeing as you told me they were all dead-"

"I did that for your benefit my dear Sameen. They abandoned you and you refused to move on. I understand your surprise, but I trust their presence won't be a problem?" Greer smirked.

Shaw sighed heavily and pulled the phone from her ear. She swallowed before pushing it back to the side of her head, "No. No, it doesn't change the mission," she replied hollowly, like a good soldier.

"Good. Besides, this may prove…advantageous."

Shaw felt an unconscious shiver run up her spine at his words. Nothing good had ever happened after he used that tone.

/Location: Unknown

XXXXXXXXXXXXX

1427 EDT

9 SEP 14/

 _Correction. Duty. Authority. Order._ The words repeated themselves over and over on the shiny white screen in front of her.

Shaw sighed. This was boring as fuck.

The door to her right squeaked open and Shaw winced as she turned to look at who it was. She grit her teeth in frustration, her wounds from the Stock Exchange were taking too long to heal. Greer walked in. Martine and Lambert lingered by the door.

"Good day Sameen," Greer said evenly.

"Would be a better one if you didn't call me that," she smiled thinly, jerking against her restrains for emphasis.

If Greer heard her he didn't react.

"Would you kindly tell us where your Machine is located?"

"No."

"Would you be so kind as to –"

"No."

"-enlighten us on how Ms. Groves communicates directly with your Machine?"

Shaw sighed and closed her eyes momentarily. She turned back to Greer. She knew where this was headed. Being taken alive by the enemy only meant one thing. She grit her teeth. If they'd just hurry up and try and hurt her, she had a chance to force their hand. It was a small chance, but it was the only out she saw. They'd need weapons and tools to hurt her. She couldn't fight off all of Samaritan, she'd already tried, but she'd settle for killing Martine before they put her down. Maybe, if she was lucky, they'd simply do it wrong. She was still weak from the Stock Exchange, if they misjudged their use of force…well they couldn't get much out of her corpse.

"You wanna hurry this along Greer," Shaw growled.

He stared at her for a long moment, unblinking, "Your point, Ms. Shaw."

Shaw grit her teeth. "You're going to torture me. So stop beating around the bush and just do it," she said grimly, leaning towards Greer as much as she could, balling her hands into fists to keep them from shaking with nervous energy.

"Ugh, finally. I said that weeks ago," Martine muttered. Greer raised a hand to silence her and she pouted.

"You're right Ms. Shaw, it does seem rather inevitable at this point. However after saving your life at the stock exchange, I had hoped we could reach a civilized agreement," Greer said quietly.

Shaw almost laughed. "You saved my life. Right, right," she muttered.

Greer sighed, sounding thoroughly disappointed. "Just remember my dear Sameen, everything that follows could have been avoided." He nodded his head once and Lambert stepped forward. The younger Brit had a sick smirk on his face and Shaw clenched her jaw.

"Something happen to your face pretty boy?" she hissed when he got close. His grin only widened. He ran a hand over the long burn mark that covered most of his left cheek

"I believe you did this to me at the Stock Exchange Sameen," he forced her neck to the side, jabbing a needle into it, "Luckily, I'll have plenty of time to return the favor."

/Location: New Jersey

40°39'08.7"N 74°13'00.4"W

1900 EDT

11 MAY 15/

The rocket launcher may have been a bit much. She watched intently as the flames billowed across the overturned car. Someone crawled out. She sighed and moved forward.

The bald one tried to help the other out of the car. They limped towards an alley way. Shaw strolled towards them, screwing her silencer into her gun. The bald one moved better than the other, but refused to leave the other man behind.

She grit her teeth and aimed her gun, putting two into each of them at center mass. She walked over to where their bodies had fallen. The bald one was still breathing. He stared up at her defiantly until the tip of the silencer was inches from his face. He nodded to himself, glancing towards his dead friend before looking back to her. "Ok," he said quietly and she put a bullet between his eyes.

"Alright, hands up," the voice startled her. She wheeled around, gun aimed high, and adjusted her aim just in time to send the bullet wide of center mass as the voice registered with her.

Clutching his shoulder, he fell to the ground, wheezing heavily. He was covered in blood and he had a head wound. He stared up at her, eyes wide. "Shaw?" his face broke in confusion and grief and she had to resist the urge to roll her eyes. She kicked his gun away.

"Lionel," she said quietly, leveling her gun at his face.

"What the hell are you doing?" he asked her. There was pain in his voice and Shaw doubted it was just from the gunshot wound.

"Stay down," she muttered, barely moving her lips. Her eyes skimmed the parking lot. He'd gone down just out of the cameras field of view. Good. That made this part easier.

"No, you just- you just murdered Carl Elias. Why?"

Shaw rolled her eyes and moved her gun so it was pointed at his head. He stopped talking, staring at her angrily, like he wanted to kill her. She blinked, her jaw tightening at the realization.

"Don't make me shoot you again Lionel," she said evenly. She'd already spent too much time with him.

Fusco's nose flared angrily. "No, you wanna kill me Shaw, you go right ahead. You look me in the eye when you do," he hissed.

She rolled her eyes and pulled the trigger. "To be fair, I thought you were already dead."

Shaw pivoted back to the bodies and pulled her knife and twirled it between her fingers as she analyzed the scene. She sighed. Make it look like a car accident, those were the orders. That meant retrieving her bullets and staging the scene.

The rocket launcher had definitely been too much.

/Location: Unknown

XXXXXXXXXXXXX

1100 EDT

21 OCT 15/

Shaw gasped for air, her whole world spinning. She shook against the restraints above her head, unable to support her own meager body weight.

"That's enough for now Mr. Lambert," Greer said quietly.

Still unable to catch her breath, Shaw grit her teeth. Greer had been watching the entire time. He always watched.

"Of course sir," Lambert nodded and ducked out. The door clanged shut behind him and the echo reverberated around the room.

"I remain as impressed as ever at your resilience Sameen," he said quietly, staring at the pool of blood at her feet. His face twitched briefly as if he found the entire situation undignified.

She grit her teeth and said nothing. She focused on breathing, on not passing out from the pain in her shoulder.

"However, I have trouble understanding where exactly this loyalty is coming from," Greer mused. "Surely, by now, you realize that they aren't coming for you?"

Shaw grit her teeth. She had figured that out. Weeks ago. It didn't change anything. She closed her eyes, trying to control the pain shooting through every inch of her. She'd told Root, not long before the Stock Exchange, not long before the kiss and the hail of gunfire and all the blood, that she did the protecting. And if Samaritan wouldn't kill her, then she'd just have to go on doing that.

Greer smiled. "It's impressive, this loyalty of yours. If entirely misplaced."

She glared at him angrily, willing herself not to puke.

Greer smiled. "After all this time, you continue to guard their secrets, to protect your Machine, and for what? They've abandoned you. You were a good soldier, valuable, but ultimately expendable."

She flinched and Greer tilted his head. "Seems I've struck a nerve," he murmured.

"I think that was Lambert, actually," she croaked, her voice hoarse from hours- from days and weeks -of screaming.

Greer smiled. "I don't think we'll be needing Mr. Lambert's assistance any longer." Shaw felt a shiver run down her spine. That was not a good tone. "Martine, would you come here a moment?"

/Location: New York: The Tap Bar and Grill

40°44'13.2"N 74°00'13.7"W

0200 EDT

12 MAY 15/

She didn't dare go inside. Shaw stuffed her hands in her pockets as she lurked in the shadows, watching the bars patrons, mostly women, as they shuffled in and out.

She'd started trailing Root from the subway. Shaw was sure Root had spotted her, had at least sensed that something was off on two separate occasions, but nothing had happened.

Root looked good. Well, she looked decidedly not dead. Admittedly that wasn't much of a benchmark. Shaw sighed. Mostly, Root looked exhausted.

Shaw watched as Root kicked open the back door and dragged two giant bags of garbage to the dumpster. Root wiped her hands on the god awful uniform she was wearing and slowly turned around in the alley, scanning it. Shaw tightened her jaw, her hand reaching slowly for her pistol. Had _she_ been followed? Was that Greer's game? Root frowned, seemingly content that whatever she thought she saw or heard was nothing, and she went back into the bar. Shaw circled the perimeter anyway. Unlike Root, she knew exactly where Samaritans stealth oriented trigger teams would be hiding. The perimeter was clear.

Shaw sighed. She needed to go. Staying here was a bad idea. Coming here to begin with was a bad idea. But she needed to know Root was alive. That she was _real_. She let out a ragged breathe, her throat uncomfortably tight. Shaw ignored the burning feeling inside her, the whispers in her head telling her how easy it would be to waltz across the street and into that bar, order a whiskey, throw her feet up on the table, and wait for Root's reaction. To leave _her_ speechless for once. But that wasn't the mission.

/Location: Unknown

XXXXXXXXXXXXX

1300 EDT

12 JAN 15/

The room was pitch black but Shaw knew it was spinning. Like an endless ride on the tilt-a-whirl, it had been spinning for hours, maybe longer. She didn't know when the last time was they had brought her food. But that was probably a good thing. She hadn't kept anything down in…days? Could that be right? Shaw tried to swallow but her mouth was painfully dry.

"Sweetie?" the voice was soft, but right in front of her. A cool hand was on her cheek, then another hand moved to her other cheek. "Sameen?"

She forced her eyes open slowly. The voice sounded familiar, but the words…she tried to focus through the darkness, on the dark head of hair in front of her, on the cool hands on her skin. "Sameen, you're burning up, we need to get you out of here."

"Out?" the word came out slurred. Shaw swallowed, trying to focus, trying to stop the spinning. Who would…? "Root?" she whispered, wincing at the way her voice cracked on the word. She tried again- "How?"

The hands on her face gripped her tighter. "The Machine told me," Root was breathless.

Shaw shook her head. That didn't make sense. "Why?"

"Because we need you Sameen. Samaritan is winning," Root sounded scared.

Shaw shook her head. "You shouldn't be here Root," she whispered.

"I'm not leaving you, not again," she pressed her lips to Shaw's lightly, letting her forehead rest on Shaw's as her eyes drifted closed again.

"Root, they want to know how you talk to The Machine, you can't be here," Shaw explained, trying to focus on getting the words out, on not slurring. "You need to leave."

"How I talk to The Machine? Why?"

"Your implant, they don't understand…" Shaw shook her head slowly. She was beginning to feel like she needed to puke again, but this was different. She tried to focus on the feeling, identify it.

"Implant…"

Shaw nodded slowly, "Yeah…" Roots hands left her face. She felt a needle slide effortlessly into her neck. "Root…?" The world began to spin again, faster now.

"Thank you Sameen," Root said. But it didn't sound like Root. The click of heels retreated from the room. The door to her cell screeched open, blasting light into the darkness.

It sounded like Martine.

Shaw forced her eyes open. "That was very helpful," Martine smiled at her, slamming the door shut again, plunging the room back into darkness. Shaw threw up again before she passed out.

/Location: New York

40°46'00.1"N 73°59'24.8"W

1400 EDT

12 MAY 15/

Shaw grit her teeth as she listened to the exchange of gunfire. Reese and Root had gone and put themselves right at the top of Alexi's hit list. Because of course they had. Two injured civilians had stupidly decided to come forward about the ambush from the night before. They claimed they could both put Alexi at the scene. Apparently Alexi was offended by such accusations.

Shaw sighed as she strolled down the street, stopping in front of a large white van. She glanced around quickly before she smashed the window with her elbow. At least Reese and Root had the sense to drag the fight to the shadow map.

Alexi on the other hand, was an idiot. He imagined himself a great leader of men. A tactical champion. But the only reason there weren't twelve cop cars and half a dozen federal agents on his ass right now was because Samaritan was rerouting all emergency calls in a five block radius.

But he did corner them; Reese and Root and the two witnesses they were stupidly trying to protect from a small Russian army. Why didn't they get that this was over? That they couldn't win like this?

Shaw skimmed the cars wires over each other, waiting for the spark. She smiled grimly when the car revved to life.

/Location: Unknown

XXXXXXXXXXXXX

0900 EDT

17 JAN 15/

"I want to thank you for your cooperation Sameen," Greer said coolly.

Shaw grit her teeth, fighting against her restraints. "I didn't-"

"But you did my dear," Greer nodded. "And now, Samaritans enemies are dead. Your…Machine is alone. Rendered useless and impotent without agents to do its bidding." He put his hand on her cheek and she flinched. "Your information was invaluable to the operation Sameen," he assured her, smiling at her proudly. "You were a good soldier," he praised.

Shaw went cold. Everything faded away except for Greer, standing there in front of her with that smug smile on his face. "I'll kill you," she said simply.

Greer smiled. "Ever the loyal guard dog," he chuckled. "But no, I don't think you will."

Shaw felt a smile twist onto her face, "I will," despite the dizziness and the pain she forced herself to stare at him, to make sure he knew it was a promise.

Greer shrugged. "Why? You never had any real loyalty to that Machine. Not like Mr. Finch and Ms. Groves di-"

"Don't say her name-"

"Come work for us Sameen."

"What?"

"You used to take out threats to national security for a living. You were quite good at it. We do the same thing. Just more efficiently," Greer smiled. "Samaritan could use more good soldiers."

"More guard dogs you mean," she sneered. Greer stared at her calmly. "Go to hell."

Greer nodded calmly. "Such a shame. But I'm sure a few more weeks, maybe even another month in here will help you see more clearly."

/Location: New York

40°46'00.1"N 73°59'24.8"W

1430 EDT

12 MAY 15/

Shaw inhaled deeply and gunned the van in reverse. The wall caved in way easier than she had expected and she slammed the breaks. She hopped out of the car, dusting off her jacket as soot and debris from the air settled on her shoulders. She coughed once, wincing at the pain that shot through her shoulder.

She stumbled over the beams and chunks of fallen wall until she found where they were holed up. They were bleeding and out of ammo. They stared at her, their mouths hanging open.

"You guys look like crap," she sighed. She turned back towards the truck and took two steps before realizing none of them had followed. "I'm sorry, were you not interested in an escape route because I can put this back," she gestured to the truck.

* * *

 _Welp...I'm incredibly nervous about this chapter...hope it turned out ok. Thanks for reading! 11/15/15_


	5. Back to Good

_Thank you to everyone for the reviews! They really mean a lot and keep me motivated :)_

* * *

/Location: New York: Safehouse

40°44'00.3"N 73°57'22.7"W

1530 EDT

12 May 15/

Root watched silently as Reese let Shaw back into the safe house.

"Van's taken care of," Shaw said quietly, seeming to look everywhere but at Root. "Torched it four blocks away."

"You followed?"

Shaw rolled her eyes, "Not my first grand theft auto John."

He nodded stiffly in apology. Shaw shifted uncomfortably, and Root knew it was because she was starring. Root wanted to say something, but every time she tried her throat closed up and her eyes started to burn. She had never been at a loss for words before. Root didn't do speechless, and in the last nine months she had imagined a thousand different scenarios in her head, along with a thousand different things she wanted, needed, to say to Shaw, but now none of them seemed good enough.

Out of the corner of her eye she was vaguely aware that Reese had moved back to the window to keep watch, but she kept her gaze trained on Shaw; afraid to move, to even breathe or blink in case this was all just another dream. She swallowed hard against the lump in her throat, her breathing ragged. "Sameen…are you-"

"I'm fine Root," Shaw said calmly, no anger in her voice. Shaw still refused to look at her. Hearing Shaw say her name triggered something in her chest, and Root bit her lip as a thousand follow up questions flooded her brain at once.

"How?" she whispered finally, feeling tears well up in her eyes.

Shaw's eyes snapped to hers then and her jaw clenched. "It's a long story," she said quietly.

Root forced a smile to her face, "Well we certainly have time for one," she cocked her head to the side playfully as she gestured to their accommodations. They'd probably be stuck at the safe house until it was dark, when they could move with less of Samaritans eyes watching. Shaw rolled her eyes and Root felt her stomach flip. She'd missed that so much.

"We don't have time for that," Reese said gravely, "Alexi's men are outside. You sure you weren't followed?"

Shaw rushed to the window Reese was looking out of, "That's not possible," she said quietly.

"We have a few guns stashed in the other room, should make for a better fight then before," Reese smiled confidently. "How 'bout it Shaw?"

"No this isn't…" Shaw was breathing heavily and Root frowned at the growing edge to Shaw's voice.

Shaw's eyes scanned the room quickly, her jaw clenched and her eyes dark. They landed on the two witnesses and she lunged for them, rummaging through their pockets as they cried out in alarm.

"Shaw, what are you doing?" Reese sounded wary.

Shaw finished on the first man and the second stared at her for a moment before futilely attempting to fight her off, kicking at her as she grabbed for his coat. Breathing heavily, she yanked his phone from his pocket. She stared at it for a moment and then swore softly.

"He fed our coordinates to Alexi," she tossed the phone to Reese. Reese read the screen, his expression hardening.

"That was a bad move Raymond," Reese said evenly. "Why?"

Roots eyes widened slightly, "He was bait." Alexi had gotten to him first, threatened and turned him, knowing that Root and Reese would come to his aid.

Shaw grabbed Raymond's head, tilting it sideways as he squirmed and protested against her.

She released him angrily, shoving him into the couch. "Figures," she muttered. Before Root could even process the motion Shaw pulled her gun and put two in his chest. The other man, Byron, screamed and cowered against the couch.

She gasped as Reese pulled his own gun and trained it on Shaw's back. "What the hell Shaw?" he growled.

Shaw rolled her eyes and clicked the safety back on. She put her hands up and spun the gun around on one finger to make it easier for Reese to grab. He yanked it from her hand and slammed her against the wall, running his hands over her body to search for more weapons.

"Left ankle," Shaw offered helpfully. Reese glared at her but moved to check it, removing the small revolver strapped to her calf.

Reese yanked her around to face them, keeping his gun out but not trained on her as he let go of her arm. "Explain," Reese ordered through gritted teeth.

"He's Samaritan," she said simply.

"You just know that," Reese narrowed his eyes, glaring at her.

"Yeah, John, I just know that," Shaw sounded bored.

"How?"

Shaw sighed and moved towards Raymond's body, brushing his hair back, revealing a thin, surgical scar above his right ear.

"Neural implant. All operatives have these now," she explained quietly.

Root felt a pressure growing in her chest. "How do you know that Sameen?" she asked quietly.

Shaw sighed and brushed her own hair back from her face, "Because I know," she said evenly, letting both of them stare at the identical incision above her right ear.

Reese raised his gun on her again. Shaw sighed. Reese grit his teeth as he stared her down. "So you're here on Samaritans orders?"

Shaw clenched her jaw, her eyes darkening. "I never said it was voluntary," she said quietly.

Root inhaled sharply and she suddenly wanted to be ill. "The first time I woke up…there," Shaw sighed, shifting her weight and suddenly unable to meet Root's eyes again, "This was already done. Near as I can tell, I was one of the first to get it, to make sure the implant worked before Samaritan stuck these in all their agents' heads," she shrugged.

"So they're tracking you, right now?" Root asked, her voice thick with fear. Shaw would never be safe with that thing in her head, they needed to get it out.

Shaw scrunched her face in confusion. "No. Samaritan has access to every camera on the planet. It doesn't care about tracking data," she shook her head.

"Then what is it?" Root whispered, her voice thick. Shaw stared at her for a moment, her jaw clenched.

"We don't really have time for this," Shaw said suddenly. "Alexi's men won't wait long, we need a back way out of here…" she turned her gaze to Reese whose gun was still drawn, "Assuming I'm coming with you," she said coolly.

Reese tucked his gun back into his coat. "Of course you are Shaw," he muttered. Shaw lay her hand out silently, asking for her gun back. Reese put it in her palm but didn't let go. "You're sure you're not being tracked?"

Shaw pursed her lips. "Truthfully?" she sighed. "No. But I'm pretty sure I'd be dead by now if I was," she added grimly.

"What are you going to do with me?" the other man asked, his voice small.

"Do you have another safe house?" Shaw asked. Reese nodded. Shaw moved to the kitchen, turning all the burners on the gas stove on. "Good."

/Location: New York: Below Ground

40°42'50.1"N 73°59'53.9"W

1800 EDT

12 May 15/

Bear and Finch were waiting for them when they returned. Bear sprinted past Harold, tackling Shaw to the ground and pinning her there as he licked her face. Shaw half-heartedly attempted to push him off, fighting her way back to her knees.

"I missed you too boy," she rubbed him behind his ears as he kept slobbering all over her.

Root smiled as she observed the exchange. For the first time in almost a year, she watched Shaw's face light up with a genuine, unguarded smile on her lips. Root cocked her head to the side, a coy grin spreading across her face. "Funny, that's how I wanted to greet you Sameen," she teased, "Well, more or less." Shaw rolled her eyes but kept petting Bear for another moment before she slowly stood up.

"Then why didn't you?" Shaw asked calmly, walking past her without another word.

Root felt her mouth open slightly, her eyes widening in surprise. Spinning on her heel, she frowned as she watched Shaw greet Harold as if she hadn't just said that.

"I am…very happy to see you Ms. Shaw," Harold said, his voice tight. He offered her a smile and Shaw nodded stiffly. Reese joined them, echoing Harold's sentiment.

Shaw hesitated slightly, stuffing her hands into her pockets. She nodded again. "Yeah, you too Harold," she grunted, her eyes looking everywhere but Harold's eyes. Bear nipped at her sleeve, whining, trying to get her attention again.

Harold smiled as he looked between them. "It has not been the same without you. And Bear certainly…well, we all missed you," he stumbled over his words slightly. Root sighed, knowing exactly how he felt. What words were good enough for this? Bear continued to lick at Shaw's hand. "I don't believe he will be giving up any time soon Ms. Shaw," he smiled lightly, "We can catch you up later."

Shaw nodded slowly, her eyes shifting between the three of them. Root flinched. Harold was not nearly as subtle as he thought he was. Shaw knew she was being dismissed. Root watched as Shaw's eyes flashed angrily, but she said nothing, she just turned to Bear and walked with him towards the other end of the platform.

"Subtle Harry," Root scolded, feeling anger hot in her chest.

"I'm truly sorry Ms. Groves but," Harold sighed heavily, "Don't you find it a bit strange?"

"What?"

"That after all this time Ms. Shaw would just…appear," Harold stared at her pleadingly.

Root shook her head. "I don't care how she did it Harold. She's here, that's what matters," she said firmly. She hadn't imagined this was how she'd get Shaw back, but she wasn't going to question it, wouldn't question her.

Harold rolled his eyes in exasperation. "Samaritan had Ms. Shaw in their custody for almost a year. Who knows what was done to her," Root winced, "Or what lies they told. But whatever it was, they seem quite confident that it worked. Because they let her out," he finished, almost out of breathe.

"Shaw saved all our lives," Root said flatly, her jaw clenched. "At the Stock Exchange and today."

"These are questions we cannot ignore. Why did they let her out? How did they know about your cochlear implant Ms. Groves?" Harold challenged. "We don't know what Samaritan did to Ms. Shaw but we must accept that she cannot have come back from her experience unchanged."

"If you want to know how she got out, she deserves to be asked directly," Root challenged, glaring between the two of them.

"She's jumpy Root," Reese cautioned, his eyes on Shaw as she played with Bear.

"Wouldn't you be John?" she snapped, turning on him. She felt her chest tightening again, angry tears threatening to spill over. "We left her there with them. Lambert and Martine have both made it very clear what they were doing to…" Root felt her voice leave her and she let out a ragged breathe. "She deserves more than this," she finished, staring icily at both of them.

Reese had the decency to hang his head and sigh.

"She killed a man in cold blood," Harold said indigniantly.

Root laughed. "A Samaritan operative who we let waltz into our safe house. Someone who could have gotten us all killed."

"She claimed he was an operative Ms. Groves and she executed him instead of letting anyone question him," Harold frowned at her. "And we don't know what else she has done, how many more she has killed on Samaritans behalf before today," he added to stop her protests.

"Fourteen," Shaw said calmly. They all turned to stare at her as she leaned against the side of the train car. "Mostly gang leaders, their money men…a few warlords. Not all though," she admitted, her eyes flashed angrily.

"Sameen, you don't have to-" Root shook her head. Shaw glared at her, stopping her cold.

"Apparently I do Root," she said quietly, stepping forward slowly. Reese shifted slightly, clearly ready to defend Harold and Shaw paused, her jaw tightening almost imperceptibly. "Three months ago Greer offered me a deal. I took it. Since then, I've reported to Lambert," her whole body tensed as she said his name, "Provide support for his missions in whatever capacity he needs, usually as a sniper."

"The ambush last night, that was you," Reese said.

Shaw nodded.

Harold narrowed his eyes. "What sort of arrangement did you make with Samaritan for your release?"

Shaw stared at him for a long moment, her whole body rigid. "If they let me out I would go back to dealing with relevant numbers." Root dug her fingers into the flesh of her palms, feeling the skin split.

"Out of what?" she whispered, her heart pounding furiously. Shaw's eyes darted to her briefly but she didn't respond.

"So you didn't tell Samaritan about Ms. Groves's cochlear implant in exchange for your release?" he asked, his large eyes boring straight into her.

"Harold, stop-" Root turned to him angrily as Shaw's nostrils flared.

"No. I didn't," Shaw said darkly.

"Then how did they become aware of it Ms. Shaw? Two weeks ago she received a phone call from you," Shaw bristled. "Which lead us to a psychiatric facility upstate. Where Samaritan attempted to remove the implant from Ms. Groves head with a surgical saw and nothing else."

Instantly, Shaw's eyes darted to Root's head, surveying her for damage.

"Stop," Root hissed, stepping in front of Shaw to stare at Harold. She pivoted back to Shaw. "I'm fine Sam," she assured her. Shaw stared at her for a moment, as if she wasn't sure she believed it. Eventually she gave a curt nod and looked away. Root sighed and turned back to Harold.

"I didn't know about that," Shaw admitted quietly, staring past them as if she couldn't meet their eyes.

"This is over," Root glared at Harold, daring him to challenge her.

Harold stayed quiet a long moment, rocking slightly on his heels. "I do not want you to think I am not happy to see you Ms. Shaw, because I am. Having you gone was," his eyes drifted to Root's for a moment before his gaze snapped back to Shaw's, "exceptionally painful… for all of us. I just-"

Shaw held up a hand, "I get it Finch," she said coolly. Harold nodded again, almost looking sheepish.

"I'll leave you to settle in then," he excused himself and Reese followed quietly.

Root watched Shaw carefully. Her body was coiled, fists tight at her side, her jaw clenched. Apprehensively, Root tilted her head to the side, chewing her lower lip. This wasn't Shaw's typical anger. An anger which moved with her, chaotic but purposeful. This was still. Deathly still, like Shaw had grown too used to having nowhere to go, no way to express the rage that so often threatened to consume her. Root felt her throat tighten as the implication hit her. Shaw was too used to feeling powerless.

She reached her hand out tentatively to Shaw's shoulder. Shaw flinched and Root withdrew slightly. Shaw turned to her, a wary look in her eye. "Let me see," Root murmured, moving to close some of the distance between them. She searched Shaw's face. "Please," she added.

Shaw nodded her head stiffly, stuffing her fists into her coat pockets. Root brushed Shaw's hair back gently, running her hands through Shaw's hair more than was strictly necessary to see the small incision scar above her right ear. The four inch cut was slightly raised against the rest of her skin. She trailed a finger over it lightly and Shaw shivered.

"What is it?" she asked again, unable to keep the concern out of her voice.

Shaw shook her head. "Root…" she warned.

"If they aren't tracking you, what are they doing Sameen," Root felt her voice crack.

Shaw pulled back from her, her jaw tight. "Drop it," she said quietly.

"No," Root swallowed hard, feeling frustration build in her. Shaw rolled her eyes and stalked away to play with Bear.

* * *

 _Thanks for reading/commenting! 11/18/15_


	6. Wicked Games

_Potential TW: more mentions of Shaw's time with Samaritan._

* * *

/Location: New York

40°42'16.8"N 73°55'15.6"W

2000 EDT

12 May 15/

"Why am I here?" Shaw asked, sounding wary.

Root turned to her grinning. "It's a surprise."

Shaw glared at her, her hands stuffed in her coat pockets. "No thanks," she said dryly.

Root abandoned the large door and turned back to Shaw fully. "Trust me," she smirked. Shaw's eyes darkened and Root felt her smile falter slightly. "Please Sam," she said quietly, feeling her throat tighten. Shaw's return wasn't supposed to be like this. Harold and Reese were supposed to trust her, Samaritan was supposed to burn, and Shaw wasn't supposed to…Shaw deserved to be happy. Or content at least. Root bit her lip. And there was a very short list of things that put that content smile on Shaw's face.

Shaw's eyes snapped up to hers then, her jaw clenched. Root stared back at her, waiting for a response but one never came. Root nodded slowly. "Thank you," she smiled softly and turned back to the door. "You won't regret it," she promised, flashing Shaw a larger smile.

Shaw rolled her eyes. "Sure Root," she scoffed, but Root was certain she saw the corner of Shaw's lip twist into a smirk.

Root turned back to the door labeled 'Fort Knox'. The door was heavier than she expected and she grunted as she opened it. When the door opened Shaw's eyes instantly lit up and Root smirked.

"No way," Shaw shot into the room, her hands instantly reaching out for the gun in the center of the display. "What is this place?"

"Carl Elias gave us his weapons bunker…among other things," Root explained. Shaw shifted uncomfortably.

"Why?" Shaw asked, her jaw tight. She narrowed her eyes as Root shrugged.

"Samaritan tried to kill him. We kept him alive, got him out of town…long, boring story really," Root shrugged casually.

Shaw accepted her answer with a small nod and went back to running her hands over the guns on display.

Root leaned against the wall, content with watching Shaw in her element. Shaw pulled a Corner Shot grenade launcher off its wall mount. She bent the barrel and smirked at the camera. Shaw turned back to her grinning, "Always wanted one of these," her eyes flashed dangerously and Root felt her stomach flip. Shaw's eyes wandered past Root, to the guns behind her. She shoved the launcher into Root. "And one of these," Shaw sounded practically giddy. "There's only about a hundred of these left," she explained, gently running a finger over antique handgun's barrel in adoration.

"This is only the beginning Sameen," Root promised, grinning mercilessly at the shorter woman. "There's plenty left to excite you," she teased.

Shaw rolled her eyes, shaking her head slightly. Root reached for Shaw's hand to bring her further into the base, fully expecting Shaw to pull away, but she didn't. Shaw growled briefly in protest, but she let herself be lead into an even larger room, where guns lined the walls like it was Costco.

Shaw sucked in a breath as she took it all in. "Ok, this is kinda hot," she admitted, shrugging her shoulders casually.

Root felt her grin widen and she turned back to Shaw, loving the way Shaw's eyes darkened as she scanned the room, taking in every type of gun on display. Shaw's eyes were black by the time they settled on her. "I'm so glad you said that," Root smirked, as she let her eyes drift over Shaw's body. Root desperately wanted to close the distance between them, but she stayed still, listening to her blood pounding in her ears. She licked her lip nervously.

Shaw's lips crashed against hers, rocking her off balance. That seemed to be Shaw's intention, as she kept pushing until Root was flat against the wall, four different gun barrels pressed into her back, while Shaw pressed against her chest, forcing every inch of their bodies together. A shiver ran down Root's spine and she grinned against Shaw's lips before raising her hands to tangle in Shaw's hair. She dragged her nails across Shaw's scalp and felt Shaw shiver against her.

Shaw pulled back from the kiss, moving her lips to Roots neck, sucking and biting anywhere she could and Root tilted her head back to give her more access. A small moan left her lips and Shaw growled, clawing at the base of Root's shirt frantically until Root helped her remove it. Shaw brought her lips back to Roots, and Root locked her arms around Shaw's head, pulling her closer, needing to feel Shaw's weight against her, to know this was real and not just another dream.

She moved a hand to the hem of Shaw's shirt, tugging at it hard to get Shaw's attention. Shaw broke the kiss momentarily, leaning her upper torso away just enough to help Root tear her shirt over her head before moving her lips back to Root's neck.

A tiny gasp slipped past Root's lips and Shaw went deathly still against her. Root clapped a hand over her mouth, simultaneously wishing it had never slipped out while fighting the sudden urge to cry. Root swallowed hard and bit her lip.

She'd known there would be damage. That Samaritan and Greer and Martine would leave their mark but…she'd thought she was prepared. The bullet wounds across the right side of Shaw's chest she'd anticipated, even if they were bigger and angrier than they needed to be; like they'd been done carelessly and fast. The needle scars that peppered her arms weren't entirely unexpected either, Root had her fair share from her short 'visit' with Control. The burns and the long angry slashes that criss-crossed her shoulders and stomach, those Root hadn't prepared for.

"Sameen…" her voice cracked. It was the wrong thing to say.

Shaw's body slid away from her completely. Shaw refused to meet her eyes. She starred at the ground instead, her fist so tight her knuckles were white. "Stop," she said icily when Root reached out for her. Root pulled her hand back instantly and watched as Shaw found her shirt on the ground and quickly slipped it back over her head. She pivoted and stormed to the door.

"Please don't leave," Root begged, her voice cracking.

If Shaw heard her plea she ignored it, and Root listened as the sound of Shaw's footsteps faded away completely. Root let out a strangled gasp, fighting not to cry as her legs buckled out from under her and her vision blurred. She leaned her head against the wall as she sat there, curled into a ball, gasping for breath, Shaw's command echoing in her head.

Sierra. Tango. Oscar. Papa. The first time she heard that, she never should have listened.

/Location: New York

40°35'05.9"N 74°05'15.1"W

2345 EDT

12 May 15/

Shaw stuffed her hands into her coat pockets and watched her breathe condense in the air in front of her. She pressed her head into the brick wall behind her, listening to the distant sound of sirens and the various sounds and echoes of the city. A year ago the calm would have bored her to tears. Truthfully, it still did a little. But months of on and off sensory deprivation made it much easier to appreciate quiet moments like this. The first time she had been out of her cell, a reward for a two weeks without an escape attempt, Lambert had laughed at her for stopping to 'smell the roses'. She'd punched him square in the face and made a run for it. With a broken leg, multiple fractures in her left wrist, and at least four hallucinogenic drugs still in her system she hadn't made it far, but that still counted as a good day in her book. She smirked at the memory as she watched a car roll up, its headlights shining right into her eyes.

"Did you miss me my dear partner," Lambert asked theatrically as he suavely slipped out of the driver's seat.

"No," Shaw responded darkly. Lambert pouted. The passenger side door opened and Alexi stepped out, adjusting the buttons on his jacket as he did so. Shaw cocked her head in confusion. "What is this?"

Lambert chuckled. "I'm needed elsewhere I'm afraid," he shrugged.

"Where?"

"DC. With Gabriel. Something or other about the Secretary of State being uncooperative," Lambert waved his hand dismissively. Shaw nodded slowly, trying not to grit her teeth. "You're Alexi's new handler, until my return."

Shaw stiffened. "I already have mission," she reminded Lambert.

"Well now you have another," Lambert said simply. She nodded once, glad that Lambert couldn't see her hands balled into fists in her pockets. "The shipment will be arriving tomorrow morning, and Samaritan expects everything to go smoothly," Lambert looked between the two of them.

"Tomorrow? It wasn't supposed to be ready for another month," Shaw frowned, forcing down the sudden tightness in her chest.

"Well, with The Machine out of the picture Samaritan felt we could move up the time table," Lambert shrugged casually, but the look in his eye told Shaw not to question further. Shaw nodded brusquely.

"I'll need more firepower and men if I'm going to keep dealing with that…urban legend and the crazy eyed one," Alexi said suddenly. "If they show up tomorrow…"

Lambert smirked. "They won't. Sameen has you covered on that front," he assured Alexi, clapping his hands on Shaw's back. Shaw grimaced.

"It's not that easy," she said slowly.

Lambert raised an eyebrow. "Oh? Enlighten me then," he said coolly, all mirthe disappearing from his face.

"They aren't stupid," Shaw hissed, "They know that the only reason I'm walking around freely is because I've been working for you."

Lamberts grin returned, "Well you'll just have to be your typical charming self and convince them otherwise." Shaw rolled her eyes. "Ms. Groves should prove especially easy to convince I would think," he smirked as her scowl darkened, and he put his hand on her shoulder, "She so wanted to believe you'd come back to her Sameen." Shaw's lip curled in disgust. He laughed. "It's tragic really. Very Shakespearean. Or Vampire Diaries," Lambert frowned. "I've been in the states too long," he muttered to himself. "Regardless. You'll keep the…urban legend and the crazy eyed one away from Alexi's business and act as his liaison to Samaritan," Lambert shrugged. "No different than Istanbul." She nodded slowly.

"Right. Just like Istanbul," Shaw muttered.

"Well, now that everyone's been briefed, I have a flight to catch," Lambert headed for his car and Alexi followed silently. "Oh and Sameen, this shipment is vital to Samaritans operations. Do not allow your…former colleagues to interfere. Samaritan may want that intel but if they prove to be more trouble than they're worth, well, Greer says two to the head will work just fine too, whether you've collected or not," Lambert let the threat hang in the air between them for a moment before smiling again and slipping back into his car.

Shaw watched the car disappear before she realized she was holding her breathe. She let it out slowly, closing her eyes as she inhaled. Exhaustion was setting in and so was the cold. She trudged slowly across the street to the gated lot she had already scouted.

She shimmied over it effortlessly, landing lightly on her feet on the other side. She walked through the rows of semi-trucks until she found one that was appropriately secluded, and hoisted herself up onto the door frame to jimmy the lock. Then, Shaw crawled into the truck cabin and pulled a ziptie from her coat pocket and thread it around her wrist and a solid looking support beam near the cabin's cot. Giving the beam and ziptie a hard yank, she nodded, satisfied that it would hold if it had to. She shifted uncomfortably on the cot. It was stiff and the whole cabin smelled vaguely of tobacco but it would do. Shaw lay back and was asleep before her head even hit the pillow.

* * *

 _Thank you for reading/commenting :) 11/22/15_


	7. Red Hands

_TW: I don't really want to classify this as domestic violence, but this chapter has me nervous because I can see this potentially being triggering in that vein? Maybe? I apologize if my warnings are inadequate. Anyways, please read with caution and feel free to message me if you just want a recap of the chapter instead._

* * *

/Location: New York: Below Ground

40°42'50.1"N 73°59'53.9"W

1000 EDT

13 May 15/

"Where have you been Sameen," Root jumped to her feet as soon as Shaw entered the subway. She frowned. "And what are you…" She tilted her head to the side as she watched Shaw drag a giant training mat, easily twice her size, behind her.

Shaw dropped it, breathing heavily. "Don't offer to help or anything," she muttered, shooting Root a glare.

Root smirked down at her, "Watching you exert yourself is much more fun," she raised an eyebrow teasingly. Shaw rolled her eyes and kicked open the mat. Root chewed her lip as she watched Shaw adjust the edge of the mat, biting down the desire to apologize, to talk about what happened the day before. If Shaw wanted to move past it, if she needed to, then Root would wait. Having her back, having her be alive, was enough. "What are you doing?" she asked again as Shaw straightened the mat. They'd done this before. After Root's 'visit' with Control, Shaw had insisted on showing her how to defend herself properly. But why it was suddenly a priority now, Root wasn't sure. Bear wandered over to inspect the mat and Shaw bent down to pet him. Shaw's sleeve slid up her arm and Root frowned as it revealed deep, new lacerations along her wrist.

"What is that?" Root asked, already knowing the answer, that it was a cut from fighting against a restraint.

"Do you want to ask questions or do you want to train?" Shaw asked, her eyes dark. Root sighed.

"Both?" She smirked as Shaw sighed in exasperation. "I'm injured remember?" she held up her splinted wrist with a pout and Shaw's eyes darkened.

"That's why you need to train," she said through gritted teeth. She hesitated, "And I'm still a half step behind Reese," she admitted quietly.

Root raised an eyebrow. "You mean-"

"I mean I've only been back in the field a few months. Mostly as support," Shaw ground her teeth in irritation, "And I'm not as fast as I was…" she hesitated. _Before._ Root swallowed down a lump in her throat, anger and fear rolling through her in equal measure. "Don't Root," Shaw cautioned, seeing the look in her eye.

Root nodded, forcing her throat to work normally. "I suppose I can help you get back in the saddle," she smirked, knowing her suggestive smile didn't come close to reaching her eyes.

Shaw ignored the comment and peeled her hoodie over her head, revealing a black tank top. Root swallowed hard. Shaw's shoulders tensed and she busied herself wrapping her hands, refusing to meet Root's eyes.

"I killed Martine," she said finally, her voice low. Shaw paused, turning to look at her. "I snapped her neck actually," Root felt her voice tremble, "Two other operatives were trying to hold me down and…that doesn't matter, but she's gone," she finished. _She will never hurt you again._ Root bit her lip hard, determined to keep those words from slipping out. They wouldn't be appreciated.

Shaw nodded silently, staring at the ground intently. "I didn't know she was dead," Shaw said quietly. Her face twisted briefly into an expression Root couldn't identify, an odd mixture of relief and grief, but it was over in an instant and when Shaw's gaze snapped back to Root her eyes were dark and angry. "Two agents had you pinned down?" Shaw asked tersely.

Root rolled her eyes, smiling lightly, "And they still couldn't stop me," she cooed.

Shaw's nostrils flared, "Not the point Root."

"Well it's kind of the point Sameen," Root sauntered over to Shaw, invading her personal space as she reached for the tape and gloves to wrap her uninjured hand.

Shaw's hand shot out, firmly grabbing her good wrist. She waited until Root met her gaze. "That doesn't happen again. Understood?"

Root raised an eyebrow, "Are you worried about me Sam?" she whispered, the grin falling from her face.

Shaw's eyes flashed angrily and she dropped Root's arm like it burned. "Stop asking stupid questions and fight," she muttered, circling around the mat.

Root raised her hands to block and Shaw did the same. "Ok then. Where did you go last night?" she asked, throwing a left hook that Shaw dodged effortlessly. Shaw had rushed out of Elias's without a word and had spent the last twelve plus hours who knew where.

Shaw clenched her jaw and swung at Root, hitting her in her side hard. Root bit back a wince. "You actually land a hit and maybe I'll answer," Shaw growled.

Root grinned and took another swing. Shaw shrugged past it and tapped her hard on her shoulder as punishment. "Don't leave yourself open," Shaw ordered. She paused and glared, "Have you not been practicing?"

Rolling her eyes, Root adjusted her stance, raising her right hand to better block Shaw's hook. Reese had offered to keep up her training, but she'd avoided coming back to the subway after the Stock Exchange so much that they'd only had the opportunity to spar once or twice. "I'm alive aren't I?" she winked at Shaw before lashing out, swinging for Shaw's face.

Shaw ducked and came up quickly, popping her on the chin. Root staggered back, shaking her head. "You're still too open," Shaw scolded. "Remember, three-sixty defense," she nodded, waiting for Root to adjust her positioning. Shaw struck high and the blow grazed off Root's arm, sliding down to her side. Shaw shook her head, "Angle your arm more Root, if I had a knife that would've just gone into your ribs," she growled.

Root shifted her feet again and swung wide with a right hook, letting Shaw duck under the punch. As Shaw came back up Root delivered an open palm strike that connected solidly with Shaw's lip, drawing blood. Root grinned. "Where did you go last night?"

"Out."

Root rolled her eyes and took another swing which Shaw blocked. "That's not good enough," Root huffed. Shaw took a swing and Root side stepped it. Shaw swung again and Root grabbed her arm. "I expect more than one word answers," she said coolly. Shaw glared at her and quickly broke out of Roots hold. Root tried again, "Where did you sleep?"

"You need to leverage my arm more, if you're going to use that hold," Shaw explained, ignoring her.

"I'm not trying to hurt you," Root said calmly.

Shaw's eyes flashed angrily, "You didn't."

Root nodded cautiously. Before, reading Shaw had been effortless for her. For all the eye rolling and angry grumbling Shaw did, they'd had an understanding, a push and pull that had worked. But now, all she felt was off balance, like she'd walked into a familiar room but everything had been moved six inches to the left; it was off, but she didn't know how to realign the pieces.

They fell into a steady rhythm as Shaw tested her, increasing their speed slowly. Root managed to block most of the hits but when Shaw connected it didn't feel like she held much back. Their breathing was ragged, and Root could feel bruises forming on her arms and the week old bullet wound above her left hip had opened up, leaving a small wet patch on her dark shirt. She avoided looking at it or calling attention to it; the only reason they were still sparring, the only reason they were sparring at all, was because Shaw didn't know about that injury.

"You're still favoring your left," Shaw scolded after landing another hit. Root nodded, breathing too heavily to respond. "They'll see that," she swung again and Root just managed to block it. "They'll use it," Shaw swung again, making Root wince. Shaw didn't let Root recover, she swung again, and Root fell. "They'll kill you," Shaw stared down at her. "Get up," she said angrily.

Root stared up at her, her head cocked. "I think we're done Sameen," Root said cautiously. Her eyes wandered to the cable car, where Reese was watching them intently.

Shaw shook her head. "No we're not," she was breathing heavily and covered in sweat too.

Root cocked her head playfully, "As much as I enjoy watching you while you're all hot and sweaty-"

"Stop it. Get up," Shaw ordered, her jaw clenched.

Root grit her teeth and got to her feet. "I'm done Shaw," she said evenly, turning to walk away.

Shaw stalked after her, "Root," she hissed, her face inches from Root's.

"Is there a problem out here?" Reese asked lightly, stepping out of the cable car, a grim look on his face.

Root's eyes shot over to his. "We're fine John," she assured him. He didn't move. "Really."

He nodded slowly and slipped back into the cable car, still watching them intently.

Root turned her attention back to Shaw, who was still glaring at her furiously. "You need to stop Sweetie," she whispered, glad her voice came out more commanding than she felt.

Shaw's eyes flashed, her jaw clenching tighter, and then Shaw blinked and the anger was gone. Shaw backed up quickly, her breathing uneven, and yet again Shaw wouldn't meet her eyes. "That can't happen again," Shaw said finally.

"No," Root agreed slowly, "it can't." She bit her lip, unsure if she should be more concerned or frustrated.

Shaw shook her head. "No Root, you can't…they can't," Shaw clenched her jaw, her hands were balled into fists. Her jaw snapped open then shut. "They told me you were dead," Shaw said, her voice so tiny and pained Root had to physically lean forward to hear her. Shaw's eyes snapped back to her, a haunted look in her eyes. It was gone so quickly Root almost believed she'd imagined it. "That you were _all_ dead," she clarified, her jaw clenched tight. "So that doesn't happen again. Two Samaritan agents, five, whatever, I don't care. They don't get the drop on you," Shaw ordered, glaring furiously at Root. Roots chest tightened painfully and her throat refused to work. Shaw's anger swelled in the silence. "That doesn't happen again," she repeated.

Root nodded quickly, "Ok."

* * *

Thank you for reading/commenting. 11/24/15


	8. One vs Many

/Location: New York: Below Ground

40°42'50.1"N 73°59'53.9"W

1145 EDT

13 May 15/

Shaw wiped a towel across her face and raised a water bottle over her head, pouring the contents over herself. She shivered as the water dripped down her skin, cooling her off. She dried off and turned her attention to the gun lockers, pulling her Nano out of the bottom compartment. Cleaning guns had always been a good way to focus, to calm down and find clarity; she'd done it mentally in her cell countless times, using the repetition to focus through the drug induced haze Martine had forced her into and through the sheer pain of Lamberts 'toys'. She began to strip the gun apart when she heard a small groan. Shaw's eyes snapped up to Root who was wincing as she tried to clean a cut on her side. Shaw clenched her jaw. Root should have told her she was injured. Root twisted to try and get a better angle and hissed in pain. Shaw dropped her gun with a sigh.

"You want me to take a look at that?" she asked, not meeting Root's eyes.

Root blinked and shifted in her chair. "You know I like it when you play doctor," Root offered with a smile that didn't quite meet her eyes. Shaw rolled hers.

As she moved to Root's side Shaw wiped her hands off on her pants. She peeled Roots shirt up and grabbed a pair of gloves from the first aid kit. Root winced as Shaw pulled back the bandage and Shaw's eyes darkened. "You were shot?" Shaw asked evenly, trying to keep the growing anger she felt in her chest from exploding.

"I may have neglected to mention it," Root agreed, smirking down at Shaw. Shaw glared up at her. "It's just a graze Shaw."

"You should have told me," Shaw muttered before she turned her attention back to the wound. She began to clean it and Root hissed in pain, grabbing Shaw's arm. They both froze.

"Sorry," Root murmured. She let go slowly, her fingertips skimming the edge of one particularly long scar before they fell away completely.

Shaw resumed her work, trying to ignore the way Root was staring at her. She sighed in exasperation as she examined the cut. It wasn't healing right. "How many times have you ripped these?" Shaw growled.

Root smirked. "John's ripped his more," she teased, her smile faltering as Shaw's fingers dug into a sensitive spot. Root let out another small hiss. Shaw shook her head in frustration and reached for the sewing kit.

"I'm not doing this a second time," Shaw muttered, shooting Root a glare. Root simply smirked back at her; they both knew she would.

Shaw worked quickly with the stitches, doing her best to minimize the scarring, but with how much Root had already torn the wound, it would definitely leave a sizeable mark. She clipped the final stitch and rocked back on her heels slightly to inspect her work. Not bad, given how out of practice she was. She nodded to herself vaguely pleased. She taped down a new gauze pad. "Don't rip it," she muttered.

She moved to leave when Root put her hand on her bare shoulder again. "Sameen…" Roots voice was low, barely a whisper, and Shaw froze, refusing to meet Root's eyes. Root moved her hand slowly across the contour of Shaw's left shoulder, lightly tracing the jagged scars that crisscrossed it. Shaw felt her blood pounding in her ears and she wanted to move or swat Root's hand away but she couldn't. It felt _nice_. Well, when Root touched parts of her shoulder she could actually feel at least. That felt nice. She clenched her jaw, vaguely aware of the fact that she wasn't breathing. "Should I stop?" Root murmured.

Shaw's eyes snapped up to Roots. Root stared at her, her large eyes glistening slightly, and there was a small strain in her neck that Shaw knew meant she was trying to keep her voice steady. Shaw opened her mouth, not sure what answer she wanted to give.

"Bear this isn't for you!" Finch scolded from outside the train car. Shaw rocked to her feet in one fluid motion, putting an acceptable amount of distance between the two of them. Out of the corner of her eye she saw Root quickly pull her shirt back over her chest. Finch shooed Bear away from him and Shaw's eyes lit up as she saw how much food Finch was carrying. She hurried over to Finch, grabbing the pizza boxes from him.

"I got that Finch," she smirked, inhaling the scent of fresh pizza.

Finch smiled at her slightly. "I hoped you would be pleased Ms. Shaw," he said kindly.

Shaw put the pizza down on the pew and flung open the first lid. She ripped a slice from the box and sat down next to it, closing her eyes as she bit into the slice, ignoring the burning sensation as it hit her tongue. "Thanks Finch," she told him, her mouth still full. Finch cringed at her behavior but nodded once before turning back to his computer.

Root joined her on the bench silently. There was a large crunching sound as she sat down and Shaw rolled her eyes. "Really? There's three pizzas here and you're eating an apple," Shaw muttered, stuffing another bite into her mouth.

Root raised an eyebrow and smirked. "Not all of us have your metabolism sweetie," Root winked. Shaw rolled her eyes.

"Nobody has Shaw's metabolism," Reese grunted as he joined them, grabbing a piece of pizza. He leaned against the subway car and bit into it.

Shaw chewed loudly, staring at Root. She fished another piece from the top box and then kicked all the boxes down the pew to Root. "Eat," she ordered, stuffing another piece into her mouth.

"I'm fine Sam," Root assured her, a smile tugging at the corner of her lips.

Shaw rolled her eyes. "You just sparred for an hour and then bled all over the subway. You need more than an apple," Shaw kicked the boxes again for good measure.

Root raised an eyebrow, her grin spreading across her face, seemingly despite her best effort. Shaw rolled her eyes but sighed when Root pulled a piece from the box and bit into it.

Finch's eyes darted between the two of them nervously. "Yes well…we need to discuss what to do with Mr. Byron."

"Who?" Shaw asked, reaching for another piece.

"The witness from the Russians ambush. The real witness," Finch said irritably. "We need to get him out of town and hope that Mr. Ansimov won't pursue him if he no longer poses a threat. Ordinarily, I would task Detective Fusco with doing this, however, I have been unable to reach him in…well over 24 hours now."

Shaw paused, chewing slowly. "I can take care of Alexi," she said finally. All three heads turned to look at her sharply. She shrugged and bit her pizza again.

"And how do you plan to do that Ms. Shaw?" Finch bristled.

"Lambert has business out of town, he made me Alexi's handler till he gets back," Shaw said. Root stared at her and Shaw flinched, unable to meet her eyes.

Finch raised an eyebrow. "It does seem you've made quite a name for yourself with Samaritan," he said slowly. "And if you can make a call like that, it would seem to indicate that you have not yet…alerted Samaritan of your duplicity."

Shaw clenched her jaw. "Look, I can make the call or not. We have bigger concerns than one witness who can maybe id Alexi," she said icily.

"I see. And what concerns might these be?" Finch said darkly.

Shaw waited until she finished her pizza to look at him. She pulled a USB out of her pocket and tossed it to him. He lurched forward, just managing to get his fingers around it.

"What's this?"

"Plug it in," Shaw shrugged.

Finch didn't move. "I'm not going to do that," he said slowly. Shaw raised an eyebrow. "You aren't the first Samaritan operative to hand me a USB drive and tell me to plug it into our network Ms. Shaw," he stared at her intently.

Shaw's jaw clenched, and her eyes darkened. She leaned forward, "No, but I'm the only Samaritan operative who at any point over the past year could have given Samaritan the coordinates to this little hideout," she reminded him, her fists balled at her side. "Doesn't get much better than that for direct network access, does it Harold?"

Finch blinked rapidly then nodded. "A fair point," he conceded. Finch limped over to his desk and plugged it in.

Shaw leaned back against the bench and looked at Root, grabbing another piece of pizza. "You nerds really should have moved," she admonished as she bit into the slice. Root smiled thinly.

"What exactly are we looking at?" Finch asked as Shaw's recon pictures filled the screens.

Shaw sighed and sprung to her feet, wiping her slightly greasy hands on her pants.

"The Barton Neurological Institute, right here in New York. It's one of the top facilities in the country that specializes in preventative treatment measures for reoccurring or ongoing neurological ailments," Shaw explained.

"Like seizures." Root said slowly.

Shaw nodded. "Yeah. Seizures. Some other stuff too," She sighed. "You mentioned something about seeing seizure implants in a facility in upstate New York?" She ignored Roots flinch. "Well, the first wave of those implants ended up in Samaritans operatives. Everyone from me all the way up to Greer has one," Shaw sighed, her hand unconsciously rubbing over the scar above her ear. "So after sticking one in every operatives head…Samaritan fast tracked FDA approval and the first shipment of chips arrived at Barton this morning."

"That's certainly alarming news Ms. Shaw, but I don't think I understand what an anti-seizure device has to do with…anything really," Finch said slowly.

Shaw sighed, her teeth grinding together. "The implant itself is fine. It's basically a slightly cheaper version of the same thing that's already on the market. Which Samaritan can do because it doesn't care about turning a profit. It's the modified microdot that makes it dangerous," She closed her eyes. "Very dangerous."

"Why?" Root asked, her voice barely a whisper.

"If Samaritan activates the microdot it causes the implant to malfunction, triggering seizures instead of stopping them. It's… more or less a kill switch," Shaw said slowly, trying not to wince at Root's sharp intake of breathe.

Finch continued to stare at her. "Why would Samaritan install a device like that in its own agents?"

Shaw shrugged. "Decima agents used to throw themselves off buildings instead of talking to us Finch. It's always been how they operate. Now Samaritan can cut out the middle man, clean house whenever it pleases," she said darkly. "It's also why I'm given so much free reign," she admitted slowly. "One mistake and well," Shaw mimed an explosion near her head, "Boom." She shrugged.

"Why is Samaritan trying to distribute these to civilians?" Reese asked.

"Is that really hard to figure out?" Root asked, her voice tight. "Remember during the election? Samaritan targeted that man it thought was unstable, to turn him into an assassin. It could do the same thing with this, cause car crashes, cause…" Root swallowed hard, her voice cracking.

"Samaritan's real targets would become victims of tragic accidents," Finch murmured.

"It would have an entire army of unknowing hitmen," Root said, her voice devoid of emotion.

"That's true…" Shaw said slowly. "It also has some more immediate plans. The Secretary of State isn't cooperating with Gabriel."

"Gabriel?" Reese frowned.

"Samaritans Analogue Interface," Root said darkly.

"The child?" Finch sounded horrified.

Shaw rolled her eyes. "The kids an asshole Finch. Believe me," she muttered. "Point is, the Secretary of State has a twelve year old son, who it just so happens to have a preexisting seizure condition."

There was a long silence.

"Or at least, he was diagnosed with one about four months ago," Shaw shrugged in exhaustion, "I don't know if Samaritan induced it or are just exploiting the situation," she clenched her jaw.

"You don't know?" Finch sounded skeptical and Shaw felt her whole body tense.

"All I know is that Jackson Connelly is scheduled to have that implant put in his head tomorrow morning," Shaw said evenly. "And he'd only be the first."

"What exactly are you proposing Ms. Shaw?"

"I've been scouting the building. I have a way in and a way to disable the microdot."

"Sounds like there's a catch," Reese murmured.

"We can't be caught. At all. In and out without anyone getting eyes on us, without being seen on any security footage…if Samaritan for any reason suspects that something is wrong here…" Shaw shrugged, "I'll probably be, well I'd definitely be dead and more importantly, they'll move the implants, take Connelly's procedure to another facility, and you'd have no way to stop them."

"So how do we do this?" Reese sighed.

Finch blinked rapidly, his eyes shooting to Reese. "We have other matters to attend to Mr. Reese," Finch said slowly. "While certainly alarming, our immediate concern and obligation is to Mr. Byron-"

Shaw cocked her head, her voice raising angrily, "Finch this institute got the first six dozen of these implants. Within a month-"

"We cannot simply abandon Mr. Byron when a man as dangerous as Mr. Ansimov wishes him dead," he said sharply. "Everyone matters to someone Ms. Shaw," Finch added, repeating a mantra he had told them time and again.

"Isn't that what we did to Shaw Harry?" Root said suddenly, her voice low and devoid of its typical mirthe. "Put our lives in front of hers?"

"That was quite different Ms. Groves," Finch said slowly, tilting his head slightly as he tried to read Root's stony face.

"Is it?" Root shot to her feet, "We stopped looking. If we'd done things differently Sameen wouldn't have a Samaritan time bomb in her head, she wouldn't have spent months-"

"Root…" Shaw murmured, slowly moving towards the taller woman. "Not looking for me-"

Root wheeled on her angrily, "No," she spat, her voice trembling.

"-It was the right call," Shaw assured her. Root's lip twitched, her whole face almost crumbling.

"No it wasn't," Root whispered, a raw, wounded look on her face. Shaw stepped towards her, and Root stepped back, shaking her head. "No it wasn't Shaw," she repeated, her breathing unsteady. Shaw backed off, turning her attention back to Reese and Finch.

"Could two people handle Barton?" Reese asked, his voice lower and more gravely than usual.

"Shouldn't be an issue," Shaw conceded.

Reese's eyes scanned over the images on the screens and he pursed his lips. "Shaw and I will break into Barton. Root can send Mr. Byron on his way out of town," he sighed, "And after that I'm finding Lionel."

Shaw nodded stiffly. "Sounds good."

* * *

 _Thank you to everyone who has taken the time to comment, I really appreciate it! 11/27/15_


	9. On the Clock

/Location: New York

40°41'16.3"N 74°04'13.5"W

2130 EDT

13 May 15/

Shaw ground her teeth against the biting wind and checked her watch. "Take us in," she ordered. Reese nodded.

The tiny motor on their black zodiac skiff sputtered to life and Reese brought them in slowly, careful to minimize the wake. Shaw zipped up her wetsuit and grabbed a pair of goggles. Reese killed the engine and joined her.

"Personal propulsion systems and a Nemo V2 underwater drill…" Reese smirked as he inspected the contents of the dry bag. "I missed committing felonies with you Shaw," he added wryly.

Shaw rolled her eyes, feeling a small smirk tug at the corners of her lips. She turned away from Reese and surveyed the exterior of the Barton Institute one last time. The building was all large glass windows and odd angles, and the windows reflected off the waterfront in the evening, causing the water to glisten. If she had it her way, she'd rather wait till closing, pull the fire alarm and blow the entire Samaritan operation to hell, but that wouldn't really work. She ground her teeth. As Finch liked saying, there was a time for a hammer and a time for a scalpel. Lately, it had been all scalpel. She sighed. Shaw really missed hammer time.

"An underwater drill?" Root's voice drifted into Shaw's ear. "Now I'm jealous," she pouted.

Shaw closed her eyes, clenching her jaw. "Why are you on this channel Root?" Shaw asked, trying to keep her voice calm.

"Relax Sameen. Thanks to your little chat with Alexi getting Byron out of town was…boring really," Root sighed, "Now I'm just…lying around."

Shaw sighed and tied the skiff under the end of the pier while Reese finished suiting up.

"The guard change gives us a five minute window," Shaw's jaw tightened, "We need to move."

Reese nodded and kicked his legs over the side of the skiff. Shaw joined him. "On your mark," Reese said.

Shaw nodded and dropped into the river. She tapped a button and the headlamp she wore flickered to life, directing her further down until she found what she was looking for; a large drainage pipe, roughly 4 feet in diameter. It'd be a tight fit with all the gear, but it'd work. She gestured Reese over and he handed her the Nemo drill. Shaw quickly removed the bolts, opening up the grate.

She motioned for Reese to follow her and pulled out the sea-doo propulsion motor, letting it pull her up the pipe against the current. The network of pipes under the Institute was complicated. One wrong turn and they'd end up under the Lasik surgery center instead and miss their opportunity entirely.

Shaw took her time navigating through the various forks in the passage until they arrived at a square room that stretched upwards almost twenty feet. Shaw swam upwards until she was at the ceiling. She pushed herself backwards until she was in the southeast corner of the cell, directly under a grated steel manhole cover. She pushed against it, struggling with her lack of leverage, before finally wedging it open. She shoved it aside and pulled herself up through the opening enough to look around. They were clear. Shaw pulled herself out and ripped off her mask. Still dripping wet she slunk to the door to make sure her entrance hadn't alerted anyone. She crawled back to Reese and offered him a hand, helping pull him up into the room. Reese pulled his mask off and sighed.

"This really doesn't seem up to code," he muttered.

"Gee, ya think," Shaw rolled her eyes. He grunted in agreement. Shaw checked her watch, "We're making good time."

"Where are we?" Reese asked.

"Sublevel janitorial closet," Shaw muttered, cracking the door open slightly. Two guards were stationed at the end of the hall. Luckily, they were facing away from the door. However, there were another two on the level somewhere. Reese joined her at the door. "Let's go," Shaw whispered, slinking into the hallway.

They moved quietly down the hallway, away from the two guards. "We make a right up ahead," she instructed. Shaw paused, the faint sound of voices was growing louder. Shaw grabbed Reese and pulled him behind a file cabinet just before two more guards rounded the corner, saying their goodbyes for the night. The guards breezed past them completely unaware. "Through there," Shaw whispered.

The door to the supply room had a simple lock on it and Shaw had it open in five seconds. They slipped in, closing the door behind them. "Those are the crates," Shaw gestured to two large wooden boxes shoved off to the side of the room, they bore the Decima logo along the border. Reese pulled the dry bag off his shoulder, and dug around in it for the other drill. He opened the crate slowly, minimizing the noise as best he could while Shaw stood lookout.

"We're in," he declared a minute later. Shaw nodded and pulled two small laser pointers from the duffle bag. She tossed one to Reese who looked at it suspiciously. "What are these?"

"No idea what they're called. Got them in a Vigilance raid about a few months back," Shaw muttered.

Reese frowned. "Vigilance?"

Shaw nodded. "There were hold outs from the night Samaritan came online, no one Samaritan viewed as a priority but... The few guys that got away, they were hiding on a ranch in Wyoming," she paused. "Samaritan…I…was tasked with tracking them down. Neutralizing the threat. They weren't really one anymore, but it was a test," She grit her teeth. The mission had proven her loyalty to Greer and Samaritan. She'd had to kill them. Shaw didn't feel particularly bad about that, beaten or not they were terrorists, but she doubted Reese or Finch would feel the same. She focused on the device in front of her, suddenly not wanting to look at Reese.

Reese nodded slowly. "Sometimes we have to make hard choices," he said quietly. Her jaw tensed and she nodded once. "So, what exactly do these things do?"

"Vigilance used these on RFID chips and cameras to jam them. It'll fry the microdot without damaging the actual implant…supposedly," she explained.

"Supposedly?" Reese cocked his head.

"It'll work," she sighed. "Just shine it over the microdots." They began waving the laser over each of the packaged implants.

"Is this supposed to do something?" Reese asked. "So we know it works?"

"No," Shaw said, her jaw tight. They had no way of knowing for sure that it worked. "If there was any visible change Samaritan would know," she added. Reese nodded grimly.

"Hey Sweetie," Root cooed. Shaw ground her teeth together before she put her hand to her ear.

"What is it Root?" she muttered as she skimmed the light over each microdot.

"While you were planning this little heist movie of yours, did you look into a Dr. Wexler?" she teased.

Shaw frowned, not liking where this was going. "The woman doing the procedure on Connelly tomorrow? Yeah…" Shaw clenched her jaw, "Why Root?"

"Oh, no reason, just wondering what her maiden name was," Root's voice was too smooth, too sweet. Shaw narrowed her eyes.

"Carson," she said slowly.

"Mmhmm…and does she have any pets?"

"Root," Shaw hissed. "Where are you right now?"

Root was silent for a long moment, "In Wexler's office," she admitted.

Shaw's hands balled into fists and she swore to herself. "Her home office I assume, because I know you wouldn't be stupid enough to break in to the Barton Institute right above us?" Shaw's knuckles were white and she felt a raw, hollow rage in the pit of her stomach.

"I can yes, if that'll make you feel better Sam," Root offered and Shaw could hear the smirk in her voice even through the earpiece.

"Root, that wasn't the plan," Reese added, shaking his head.

"Did you really expect me to stay out of this John?" Root snapped. Reese sighed and shook his head again as he kept scanning the microdots.

"What. The hell. Are you doing?" Shaw bit out, barely able to contain her fury. She could barely breathe, barely speak. Root could ruin the mission, could get herself killed, could ruin _everything_ in an instant.

"Research," Root said, her voice suddenly serious. "You know, I've done the whole silent breaking and entering thing before Shaw, I'm pretty good at my job," she added, no hint of levity in her voice.

"Root get out of there. If anything goes wrong-"

"You'll die. I'm well aware of the stakes Sam," Root said darkly.

Shaw clenched her jaw and shook her head incredulously. "Leave. Now," she hissed.

"I'm copying her files and I'll be out in a moment," Root said calmly.

"That's all of them, we're done here," Reese announced, moving the lid of the crate back into place. He drilled the bolts back in careful to make it look like the crate hadn't been opened.

Shaw looked at her watch and growled. "Guard change is done by now." Reese nodded gravely.

They slid back out into the hallway and easily avoided the two guards that were roaming the hall. They rounded the corner back to the supply closet and froze. One guard was standing in front of the supply room, staring down at a small puddle on the floor.

"Crap," Shaw hissed. They'd been dripping wet when they'd gotten out. The puddle wasn't sizeable, but it was out of place. The guard frowned slightly and walked into the janitor's closet. He emerged with a cart and mop and scrubbed the spot down. He nodded to himself and pulled a wet floor sign from next the cart. The guard smiled, clearly pleased with himself. He pushed the mop and cart back into the janitors closet and moseyed down the hallway whistling.

Shaw exhaled heavily, feeling her heart rate slow. "You may have overestimated their security Shaw," Reese muttered, smirking. Shaw glared at him before moving for the supply closet. They rushed forward and popped the manhole cover off again. Making sure to seal the cover behind them, they dropped silently back into the water and navigated their way back out into open waters.

Shaw crawled into the zodiac and pulled off her mask, her teeth chattering as the cold wind hit her face. Reese climbed up behind her.

"Hey guys," Root's voice drifted into her ear, "Any chance I could have a ride? I'm just around the corner."

Shaw grit her teeth.

"On our way Root," Reese said calmly.

Reese navigated the boat around the pier to another low dock. Root was standing on the end, her arms crossed across her chest as her hair whipped around her in the wind. Reese offered his hand and Root hopped into the skiff.

Shaw starred past Root, refusing to meet her eyes. She clenched her fists, determined to keep her teeth from chattering. Root stared intently at her phone, her eyes rapidly skimming over the new data she had stolen.

"Find anything useful?" she asked icily.

Root blinked and looked up at her. "Not yet Sam," she said, smiling smugly.

Shaw growled and clenched her hands tighter, determined to resist the nearly overpowering urge to push Root overboard.

* * *

 _Thanks for reading/commenting! 11/30/15_


	10. Woman and Machine

_A special thanks to my new beta! witheveryheartbeat/broodystars (archive of our own/tumblr)_

* * *

/Location: New York: Below Ground

40°42'50.1"N 73°59'53.9"W

0100 EDT

14 May 15/

Root stared at the screen in front of her intently. She could feel Shaw's eyes on her, glaring daggers at her back as she stalked up and down the subway station. She'd already been over the data from Dr. Wexler's office twice, but Root refused to admit defeat. It couldn't be nothing. There were codes and access information for all of the implants the Barton Institute had received, but nothing in the files gave her any idea how to access or disable the one in Shaw's head. She hadn't expected to find the solution by breaking in, but a lead…something. She smiled bitterly. Drugging Shaw and sticking her in a Faraday cage suddenly seemed like the best and only option. And she doubted Sameen would appreciate either part of that plan. Exhausted and frustrated, Root leaned forward, resting her palms against her eyes.

"Find something useful?" Shaw's voice was biting and sarcastic.

Root rolled her eyes, using the moment to steady her voice. "No," she admitted quietly.

"Huh, well there's a surprise," Shaw hissed.

Root's vision blurred and she shook her head, "What do you want me to say Shaw?" she asked quietly. "I'm not apologizing for this," she added, turning to face Shaw, her arms crossed defiantly.

Shaw scoffed and surged towards her. "How about you admit that you can't pull this kind of crap anymore? You don't have The Machine in your ear anymore Root. It's gone. You're on your own. And if you had been seen on camera for even one second," Shaw shook her head and backed off. "You have no idea what would have happened."

Root bristled and launched out of her chair, "I know exactly what would have happened," she stared down at Shaw angrily. "I am not watching you die again," she spat, forcing the words out before her voice stopped working entirely. The memory flashed across her mind, a kiss, three gunshots, blood, screaming, that damn gate separating them while she screamed herself raw and her heart was ripped from her chest. Root let out a ragged breath, trying to force the images away.

Shaw rolled her eyes and shook her head. "Do you know how long it takes a Samaritan trigger team to respond?" She inched closer to Root. "Because I do. I've led them." Root glared at her. "And with or without The Machine in your ear, you're a target they would want alive," Shaw moved closer, her eyes still dark with fury, "And you may not know how Samaritan treats their guests, but I do," she hissed. "So no Root. You don't have a clue what would have happened." Shaw shook her head in disgust and stalked away.

Root smiled bitterly and wiped hastily at her eyes. "You're wrong you know," her voice waivered but Shaw paused. "The Machine is alive. Barely, but…this isn't over Sam," she promised. "We're not done fighting."

Shaw turned back to her slowly, surveying her, her expression guarded. "The Machine isn't gone?"

Root nodded, not trusting her voice. She pointed to the cable car. "The briefcase," she muttered, her voice cracking.

Shaw frowned and stalked into the car, opening the briefcase. The Machine whirred to life, identifying Shaw as a primary asset. She beeped once and the word ' _Hello_ ' appeared on Her screen. Shaw scoffed. Root walked into the car slowly, and stood over Shaw. Shaw stared at Her before turning back to Root. "How is this even possible?" she asked. "We saw where they kept The Machine before, it was massive…"

"This is just Her base code. Her memories, Her morals," Root stared at the box sadly, "Her eyes and ears are gone. She's trapped here with us, wasting away," Root sighed in frustration.

Shaw nodded slowly, "Right, well, I'll pretend that makes sense," she muttered.

"Harold and I are trying to get her back online fully," Root grit her teeth, "It's…going slowly, but when we do…" Root sighed, her voice thick, "Maybe…" she shook her head, "She will know what to do about that implant," Root stared down at Her angrily, "She has to."

Shaw raised an eyebrow, silently watching Root. She sighed and the anger seemed to disappear from her body, leaving her looking exhausted. "Root, by the time you get your favorite robot overlord back online I won't be here," Root turned to her, "Samaritan won't keep me in New York for long. Fixing this," she gestured to the scar on the side of her head, "Is not a priority."

Root felt her stomach lurch. She hadn't thought about Shaw being forced to leave. She hadn't let herself think about the doomsday clock hanging over their heads again. Her chest felt tight and it was hard to breathe. A wave of panic washed over her, she was running out of options, out of time. Again.

Root surged forward, crashing her lips against Shaw's as her hands grabbed fistfuls of Shaw's tank top, refusing to let her go. Root felt fingers against the back of her neck, as Shaw wrapped a hand around her back to leverage herself up and into her. Shaw's other hand was on her hip, pressing them together as Shaw dragged Root across the car to an empty table. Shaw lifted Root onto the table, her hands sliding under the hem of Roots shirt, gripping her hips tightly.

"This is a bad idea," Shaw whispered against her lips and Root blinked, her throat tight. Shaw pulled back slightly, staring at her intently, her eyes dark. Root felt her stomach flip. Shaw was frowning but there was no anger in her eyes.

"You want to stop?" Root whispered, her eyes unconsciously traveling to Shaw's bare shoulders.

"No." Shaw's voice was raw, strained. "But this only ends badly," she said quietly.

"Only if you're doing it wrong, sweetie," she grinned sweetly and watched as Shaw rolled her eyes.

"You know what I mean Root," Shaw grumbled, staring straight into Root's eyes.

Root let out a ragged breathe. "I can take care of myself Sam," she assured her, wincing as her voice cracked. She'd already lost Shaw once, she knew she couldn't do it again. She wouldn't.

She leaned forward, pressing their lips together again. Shaw hesitated before giving in, tightening her grip on Root's hips. Shaw trailed kisses down Root's neck, nipping lightly at the base, and Root let out a whimper. Shaw pulled back suddenly, with a growl and stalked over to The Machine. She slammed the lid closed before coming back to Root, tearing at the buttons on Root's shirt.

"Concerned about my modesty?" Root's smirk turned into a groan as Shaw began to kiss and bite her way down Root's exposed skin. Root felt her breathing grow uneven as she leaned into Shaw's touch, her head spinning as Shaw's presence consumed her. Shaw's hands made quick work of the top buttons on her shirt before fumbling at her stomach. Growling, Shaw yanked on her shirt and Root was vaguely aware of the sound of buttons bouncing on the ground. "I liked that one," she protested weakly, even though she didn't give a damn. Shaw growled against her neck and Root grinned.

"Shut up," Shaw muttered, bringing her lips back to Root's. Shaw's hands slid across Root's stomach, making her shiver. Her mouth followed, kissing a trail down Root's stomach while her hand shoved aside Root's bra, pinching her nipple hard enough to make Root groan. Shaw's eyes darted back to hers, a small smirk tugging at the corner of her lips before she leaned up to capture Root's mouth again. Shaw pressed against her as her hands skimmed up and down Root's body before they slipped under her pants, and Root gasped as fingers slid into her.

Her grip on Shaw's shoulders tightened as Shaw's fingers worked in and out of her, her palm pressed to her clit, while Shaw's lips continued to bite and suck at her neck. Root closed her eyes, her hips bucking and rolling against Shaw's palm. Shaw's breathing was ragged against her neck and Root felt her throat tighten, feeling dizzy. She'd dreamt of having Shaw back, of Shaw's hands and mouth being exactly where they were now. The reality was so much better. So much more. And she could lose it all over again. Panic began to seep in through the haze until Shaw's mouth moved to her ear. "Root," she whispered, her voice thick in a way Root had never heard before. Root whimpered and her hips bucked as she came against Shaw, shaking. Root lay her head on Shaw's shoulder, breathing hard. Shaw pulled her hand away, wiping it on her pants before resting it lightly on Root's hip.

Shaw's face remained buried in her neck, the heat of her breath tickling her neck. Placing one delicate kiss against her clavicle, Shaw sighed. Root felt the sting of tears in her eyes and sniffed, determined not to let them fall. That was not how this was supposed to end. Terrified of Shaw's reaction she pulled her head from Shaw's shoulder to see the smaller woman staring at her intently, her brow furrowed, but there was no anger in her eyes. Shaw tightened her grip on Root's hips and Root let out a sob, burying her head in Shaw's shoulder.

/Location: New York: Below Ground

40°42'50.1"N 73°59'53.9"W

0630 EDT

14 May 15/

Root groaned as she woke up. She shifted against the flimsy mattress below her and frowned in confusion, not remembering how she'd gotten there. The subway was pitch black except for a small glowing light coming from inside the train car. She sat up slowly, cold air hitting her bare chest. Her shirt was still wide open. She shivered and pulled the blanket from the bed with her as she moved towards the light. Shaw was sitting in front of the open briefcase, her shoulders hunched.

"You got anything to say to me?" Shaw asked Her. The Machine's screen remained blank and Shaw scoffed. "Yeah. That's what I thought," Shaw muttered angrily.

Root bit back a grin as she stood in the car's doorway. "Talking to your robot overlord Sam?" she teased.

Shaw turned to her, her scowl disappearing. "Your machine isn't exactly chatty," she said irritably.

Root smiled bitterly. "Not when you need her to be," she agreed. Shaw cocked her head, her eyes narrowing. "She told me to stop looking for you," Root explained quietly. "And I listened," she added, her voice cracking.

Shaw blinked, then nodded slowly. "Good," she said. Root's stomach dropped. Shaw sighed. "You had to trust The Machine Root…you have to…even now," she said quietly, her eyes dark as they drifted back to the open briefcase.

Root frowned, chewing her lip as she pulled the blanket on her shoulders around her tighter. She did trust Her, even if her faith was shaken, she trusted The Machine completely. But Shaw had never shared that faith. "How can you say that? After…everything," she finished lamely.

Shaw shrugged, "It was the right call," she assured her yet again, staring up at her from Harold's chair. Root watched as Shaw's fists clenched and unclenched at her sides. "You would have gotten yourself killed," Shaw reasoned. "You would have died and then The Machine would have died, and it would all have been for nothing."

"Not for nothing," Root said quietly, her head snapping up to stare directly at Shaw. Shaw averted her eyes, her entire body tensing under Root's gaze.

"The Machine is more important Root," Shaw said quietly, staring past Root, unable to meet her eyes.

Root's chest tightened painfully and she let out a ragged sigh. A part of her believed that. The Machine was more important than any of them. She was more important than _all_ of them combined. If Harold would let her, She could save all of human kind. She was perfect.

Root stared at Shaw, at the way Shaw's jaw clenched and unclenched slightly, like she was fighting with herself. Shaw was imperfect, angry, and clearly more unsettled by her time with Samaritan than she cared to admit, but she was still Shaw. And somehow, Shaw had become the single most important person in Root's entire world. And The Machine had failed Shaw. And Root had let Her.

Root swallowed hard, forcing her voice to come out stronger than it had been, "I should have protected you." At the Stock Exchange and after. Always.

Shaw's eyes flashed angrily. "That was never an option Root," she growled and rolled her eyes before stalking past Root and out of the car.

A loud bang startled both of them, and Shaw shoved Root into the train car for cover, pulling her Nano from the waist of her pants. Reese flew through the door, his gun drawn and trained on Shaw.

"What the hell did you do Shaw?" Reese yelled as he crossed the platform.

Shaw sighed and dropped her gun, raising her hands into the air in surrender. Reese ignored the gesture and slammed Shaw against the train car, lifting her off her feet. He dug the gun into her stomach and she stared at him defiantly. "I'm only going to ask this once," Reese hissed, his voice pained, "Did you murder Fusco like you did Carl Elias or did you just hand him over to Samaritan?"

* * *

 _This fic is officially at the halfway point! Yay! Thank you guys for all your awesome comments/support. 12/07/15_


	11. Smoking Guns

_Sorry for the delay everyone. It's been a hectic few weeks! :) Hope everyone who had finals/midterms etc is doing ok!_

* * *

/Location: New York: Below Ground

40°42'50.1"N 73°59'53.9"W

0715 EDT

14 May 15/

There was a hollow feeling growing in Root's stomach. "What are you talking about John?" Root asked, the blanket around her shoulders fell to the floor silently and she shivered. She felt stuck in place, staring as Reese held Shaw against the side of the train car, her feet dangling almost a foot off the ground. She was vaguely aware that Harold was lurking behind her by his desk, quietly watching the entire exchange.

Reese kept his grip on Shaw, refusing to avert his eyes, "I tracked the route Fusco took out of town with Carl Elias. He knew what he was doing, it was all backroads, to avoid crowds and cameras. But they stopped for gas in this little town in the middle of the night. Quarter mile past the gas station there was an accident. One car, two bodies. Just a couple out of towners passing through. No one thought anything of it. But I checked the cameras," Reese shook his head, a menacing smile on his lips, "It wasn't an accident. Shaw executed Carl Elias. And his business partner. And Fusco."

Root turned to Shaw slowly, watching Shaw's jaw clench and her eyes darken. "That's not possible," Root said quietly.

Reese whipped his head around to her angrily. "It's all on tape Root," he growled before turning back to Shaw, "Did you not know about the camera Shaw? Or did you just think Samaritan would protect you?"

"Samaritan only considers it a confirmed kill if it's on camera," Shaw said calmly. "I knew it was there."

Root let out a ragged breathe as the room started to spin. "Sameen…"

Reese's face contorted in grief and rage, "We trusted you." He dug his gun further into Shaw's ribs, until her jaw clenched from the pain.

"I'm not going to lose sleep over killing a mob boss John," Shaw said, her voice still eerily calm.

"And Fusco?" Reese hissed.

Shaw shrugged, "Not losing sleep over that either-"

Reese growled and slammed Shaw back against the train car before throwing her to the ground.

Shaw sat up slowly, a bitter grin on her face. Reese leaned down over her, grabbing her shirt, and struck her across the jaw with a sickening crack.

"That's quite enough Mr. Reese," Harold said suddenly.

Reese staggered back, breathing heavily. Shaw rubbed her thumb against her cheek, checking the damage and leaned over, spitting blood onto the ground. Root stood in place numbly.

"I'm not losing sleep because Fusco isn't dead," Shaw said icily. "Well, I've never actually lost sleep over anything but you get my-" Reese lunged for her again, lifting her to her feet. He slammed her against a pillar and Shaw winced. "Do that again and I'm gonna lose my patience," Shaw hissed.

"You shot him Shaw," Reese shook his head, "I saw the security footage."

Shaw nodded. "I didn't know he was in the car with them. Lionel came up behind me and I clipped his shoulder," she shrugged. "The second shot was for show. Scared him, didn't hit him."

Harold stepped forward, his face neutral. "The footage was quite convincing Ms. Shaw," he warned.

Shaw rolled her eyes. "Yeah Finch. It was supposed to be," she sighed. "Have you found Lionel's body?" she asked.

"No," Reese admitted, tightening his grip on Shaw's collar for good measure.

"Right, because he's not dead," Shaw growled.

"Then where is he?" Harold asked, tilting his head slightly as he surveyed her.

"Can't tell you that," Shaw shrugged.

Reese shook his head. "That's my partner you shot Shaw. Now, maybe you've forgotten what loyalty is," Shaw's jaw clenched, "But we haven't. We aren't losing anybody else. So you're going to tell me where Lionel is," he growled.

A smirk spread across Shaw's face, "Is that a threat John?"

"If it has to be," he said quietly.

Root glanced between them silently, blood pounding in her ears. None of this made any sense. Shaw wouldn't betray them, wouldn't betray her. She knew that, as profoundly as she believed in The Machine. She inhaled shakily.

"Lionel is safe," Shaw said slowly.

Reese shook his head, "I need a lot more than that."

"Sam, please…" Root stared at Shaw, trying to make sense of what Shaw was doing, what game she was playing.

Shaw rolled her eyes, unable to meet her gaze. "That's not gonna work Root."

Reese was silent for a long moment, breathing heavily as he pinned Shaw to the wall. He sighed and let go, letting Shaw's feet sink back to the floor.

Shaw sighed, "Good," she shook her head. Reese grabbed her left wrist and yanked it behind her and upwards. Shaw hissed and threw her head back, hitting Reese in the nose. He growled and yanked further at her arm until there was a popping sound and Shaw gasped in pain. He drove her to her knees, breathing heavily. Reese pulled his cuffs from his belt and shackled her good arm to a solid pipe. Shaw glared at him murderously. Root glanced down at her feet, where Shaw's Nano lay forgotten.

"You can tell us willingly or we can get the information out of you," he said darkly.

"If you think you can get something outta me that way go ahead," she hissed, her lips twitching upwards in a vicious smirk. Root felt her stomach churn. How many times had Shaw used that expression in the past year; how many times had she directed it at Greer, at Lambert, at Martine? She leaned down slowly, her fingers brushing the cold metal of the Nano.

Reese smirked bitterly, "I know I can Shaw. Samaritan did." Shaw's eyes flashed angrily, her entire body going still.

"Don't touch her again," Root hissed, raising Shaw's Nano halfway. Her hand shook slightly as she stared Reese down. They'd been through hell together looking for Sameen. It was hard to believe there was a time where she didn't care what happened to him, when she didn't care one way or the other whether or not he caught a bullet. But he wouldn't lay a hand on Shaw again. No one would.

Reese rounded on her slowly, "This is what we do to get our people back Root," he explained quietly, tilting his head at her in confusion, a wounded look on his face. "This is what we did for Shaw in Maple and we're going to do just as much to get Lionel back." He stared at the gun with an odd expression on his face. He didn't think she'd use it. She raised it higher. He was wrong.

"Shaw's one of us."

"That appears to no longer be the case Ms. Groves," Harold said darkly. "Please, put the gun down."

Root shook her head, her breathe unsteady as her heart pounded against her chest.

"Root…" Shaw sighed, "Listen to Finch." Root's eyes darted past Reese, to Shaw, who nodded to her slowly, her eyes boring right into Root's for the first time since Reese had entered the subway. Root grit her teeth and sighed. She lowered the gun to her side but didn't put it away. Shaw sighed in relief and turned back to Reese. "Besides, you're not as good as Samaritan John," she almost goaded, staring at him defiantly, and Root fought back the urge to be sick.

"We are not the enemy Ms. Shaw. And we are not like Samaritan," Harold said sadly. Reese turned to him to protest, "This is not how we do things Mr. Reese," he reminded him darkly.

"Finch," Reese sounded pained.

"Ms. Shaw will stay here. No contact to the outside world. I imagine that the longer she is here, unable to contact Samaritan, the odds of them activating that device in her head increase exponentially," Harold stared at Shaw as he spoke, watching her every movement. "If you truly have no qualms about betraying us Ms. Shaw, then perhaps you at least still care about what happens to your own head," he starred down at her with open disgust.

Shaw glared at him. "You really think you can keep me here?" she smirked.

Finch held up a black anklet with a sad smile. "I believe you remember this?" Root did. They'd put it on her in the library, to keep her prisoner. When Harold had found the time to modify the subway with a similar invisible perimeter she didn't know. He handed it to Reese and Reese walked over to Shaw slowly.

"Try anything and I break the other one," Reese threatened. Shaw's nostrils flared angrily, but she stood still while he yanked the anklet tight around her leg. He pulled a zip tie from his pocket and took her injured arm and roughly zipped it to another pipe, away from her other hand.

Harold nodded slightly, pleased with himself. Root hands were still trembling so she put the Nano down on the pew. She could barely breathe.

"Shaw's our only lead on Fusco," Reese sighed bitterly. "He won't hold up under that kind of torture Finch, not if Samaritan has him."

Shaw rolled her eyes angrily.

"We have another situation that requires our immediate attention Mr. Reese. However, while you and Ms. Groves attend to that matter, I will do what I can to locate the detective," he said decisively.

Reese tilted his head in confusion, "I'm not leaving you alone with her, Finch."

Harold blinked, "I won't be alone Mr. Reese. I have Bear," he turned to Shaw icily, "Bear won't let her hurt me. And if Sameen is really so far gone as to consider hurting Bear, well…" a small, sad smile tugged at the corner of his lips. "Then I think we could all agree that Samaritan's hold on her is deeper than we imagined." He nodded once, curtly, "So I believe we will be quite fine here, even if she somehow managed to escape her current confinement."

Root shook her head angrily and stalked forward, reaching out for Shaw. Shaw flinched away from her and Root pulled back. "Sam, please just…tell us what's going on. Tell me," she pled, her voice thick.

Shaw's eyes snapped to her and her jaw unclenched. Her brow furrowed and she sighed. "There's nothing to tell Root," she muttered.

Reese growled.

Harold sighed. "Asking Ms. Shaw to cooperate will clearly get us nowhere Ms. Groves. Let's not waste any further time beating our heads against the wall," he said dryly and limped back to his computer.

"So what's this other mission?" Reese asked, still staring murderously at Shaw.

"When I was developing The Machine, floppy drives were more widely used than USB's Mr. Reese," Finch snorted, "A decade of technology has come and gone. The Machine could never compete with Samaritan on a purely technical level. She…was always slower, by the very nature of her infrastructure. To even stand a chance against Samaritan, we must rebuild The Machine using modern technology."

Reese frowned, clearly lost. Root rolled her eyes.

"What are you suggesting Harold," Root asked, trying to be civil.

"I have been looking for advantages we can exploit if we hope to rebuild The Machine. Every tech blog, new development, every piece of hardware. Samaritan was built using what was, at the time, the fastest processor in the world Ms. Groves," he pursed his lips, "But as of last night that is no longer the case."

Root's eyes widened. "Where is it?"

"Here in New York, at a tech start up called Quantum Dynamics," Harold said slowly.

"You can't seriously be considering this," Shaw scoffed.

"Don't recall asking your opinion Shaw," Reese flashed her a hollow smile, his voice low and menacing.

"You get word that some fancy new tech just happens to be available, conveniently located right here in the city and your first thought it to charge in after it?" Shaw shook her head. "You do realize Samaritan will want it too right? Assuming it's even real and not just a trap to lure you out," she glared at them.

"It crossed my mind, certainly," Harold said indignantly, "But if we move quickly, we can-"

"No. There's nothing you can do. Nothing," Shaw sneered, jerking against her restraints furiously. "The only reason any of you are alive right now is because Greer doesn't know if The Machine is really gone," she hissed. "That is the only leverage you have and the second you show up for that processor you'll go right back to the top of Samaritan's most wanted list."

Root inhaled sharply. "Is that why you're here?" she said quietly, as the pieces sank into place, she turned to Shaw, her eyes burning, "To find out if The Machine survived," her voice shook as she stared at Shaw. Root felt her throat tighten and her face crumbled, "This whole time…" Her mind unwillingly drifted back to the night before, to Shaw's warning that this would end badly, to her sudden interest in The Machine's presence… It had all been for a mission.

Shaw stared at her blankly, her jaw tight.

"Say something Sam!" She yelled, her whole body shaking. If Shaw wouldn't even defend herself it was because she couldn't. Which meant it was all true.

"I'm sorry Ms. Groves," Harold said quietly, "The Machine…She couldn't have predicted this when She asked us to stop looking," he admitted, putting a hand on her shoulder as if that could comfort her. She shrugged it off angrily, fury building in her chest.

"Where is this processor Harry?" she asked, her voice cold. She moved into the train car, shedding her broken, button less shirt and pulling a spare from the storage locker.

Harold nodded, "Across town. You can be there in 30 minutes."

She nodded curtly, twisting the buttons on her shirt into place. "You ready John?"

Reese's eyes darted between Shaw and Finch. "Yeah," he said finally.

"Root…" Shaw's voice was low, almost pained, "Don't do this."

Root's jaw clenched. "Is it just a trap? Or is the processor real?"

Shaw opened then closed her mouth. She shook her head in frustration, "I don't know but-"

"Then just shut up Shaw," Root turned and walked away.

* * *

 _Thanks again to my beta witheveryheartbeat/broodystars (here/tumblr) and to everyone who has taken the time to comment! 12/20/15_


	12. Arms Race

_I hope everyone's holidays went well :) Person of Interest won a People's Choice Aware!_

 _(those two things are totally unrelated. But yay!)_

 _Disclaimer: I'm not a doctor. Today's medical knowledge/advice is courtesy of Google..._

* * *

/Location: New York: Below Ground

40°42'50.1"N 73°59'53.9"W

0820 EDT

14 May 15/

"We're in position," Reese's voice blared through the subway and Shaw blinked in surprise.

"Any sign of Samaritan?" Finch asked, leering at her from across the station. Shaw rolled her eyes. For whatever reason, Finch wanted her to hear it. To make her feel guilty probably. She sighed. It was like he didn't know her at all.

"No sign of anyone Harry," Root confirmed, sounding uneasy. "Maybe they open later but a company like this should have a night staff. Janitors, security…"

Pretending not to pay attention, Shaw shifted as far out of Finch's line of sight as she could get. She winced as a wave of pain shot through her left shoulder. Inhaling deeply, she closed her eyes and leaned her left shoulder forward, letting gravity pull it down. She bit the inside of her cheek to keep from groaning and slowly rotated her shoulder backwards until she felt the pop of her shoulder relocating. She hissed and stood back up, testing her mobility and range as best she could while handcuffed to two separate pipes.

Bear trotted over to her and tilted his head in confusion. He let out a low whine and Finch turned to her, glaring.

"I know boy," she muttered.

"Proceed carefully then Mr. Reese," Finch cautioned, still staring at her.

Shaw sank to the floor and leaned her head against the stone pillar in frustration. Bear trotted over and sat at her feet. Shaw tugged on her cuff as much as she could, just managing to get a hand behind Bear's ear. She scratched it affectionately and he panted happily.

"We found it Harry," Root announced, whistling. "Wow this processor it's…"

Root cut out, leaving the line buzzing with static. Finch bolted upright in his chair. "Ms. Groves?" Shaw paused, grinding her teeth.

Root contacted them a minute later. "I'm fine, we both are, but Alexi is here."

"Mind asking Shaw what her asset's doing here?" Reese growled.

Her jaw clenched angrily as Finch turned to look at her. "Care to enlighten us, Ms. Shaw?"

Shaw shook her head, "I don't know, Finch." She sighed. "How many?"

"How many men are you up against?" He repeated.

Reese sighed angrily. "At least six in the building. Another two vans blocking the exits, probably another dozen outside."

"That's too many for a trigger team then," Shaw explained, gritting her teeth. "You haven't tripped any alarms, but whatever they're doing there is planned. Samaritan might've just sent Alexi to retrieve the tech. Same as you." She grit her teeth, "Or it's a trap," she admitted.

"I have an idea Root," Reese muttered, his breathing heavy.

Finch nodded slowly. "Ms. Shaw seems to believe that Alexi has been sent for the chip and may not be aware of your presence."

"Oh," Reese said quietly. A loud explosion rocked the line. "They know now," he added dryly.

Shaw inched her way up the wall slowly and sighed. Reese and Root were good, but taking on two dozen Russians who had them pinned down was still a suicide mission. She glared down at her left hand. Her shoulder injury would already slow her down, breaking her thumb really wouldn't help. But with how Reese had locked her up it was her only choice. She pressed her thumb into the side of the pillar, tweaking it until she heard a popping sound and her vision flashed white. She grit her teeth, pushing back a growl and slipped her hand free of the cuffs.

"Two more down. Finch any idea how we should get out of here?" Reese yelled over the sound of bullets. Finch scrambled to his keyboard.

Shaw moved her hand to her combat boot and pulled a small pin out of the rubber sole. She forced it into the keyhole of the other cuff, cracking it open in seconds. Careful not to alert Finch, Shaw slid the cuff silently to the ground.

She looked to the ankle bracelet Reese had forced her into. That would be harder to get off. The sounds of Root and Reese's fire fight echoed through the subway and she sighed. She didn't have time to figure a way out of it. Shaw moved quietly to the train car, pulling her Nano from the pew and a M4 carbine from the storage locker.

"What are you doing Ms. Shaw?" Finch asked suddenly, bolting from his chair.

Shaw sighed and rolled her eyes as he moved away from her fearfully. "Relax Finch," she muttered.

"What's Shaw doing Harold?" Reese asked.

Finch's mouth opened then closed. "Nothing. Nothing Mr. Reese," he touched his ear, cutting the line.

"They're in over their heads Finch," Shaw said angrily. "Cut this thing off my leg," she gestured to the anklet.

Finch straightened slightly, determined. "No, I won't do that," he said evenly.

Shaw rolled her eyes and turned for the door. "Fine," she growled, staggering as she hit the perimeter and the first electric jolt ran through her. She sunk her teeth into her lip, refusing to cry out, letting the current pass, and pushed forward until another wave of voltage made her crash against the wall.

"I'm afraid they will only get worse Ms. Shaw," Finch cautioned.

Unsteadily, she continued up the stairs. She turned to him, smirking bitterly. "Good thing I've had some practice with this sorta thing huh?" Besides, the battery had to run out eventually.

/Location: New York: Quantum Dynamics

40°42'44.1"N 73°59'18.8"W

0840 EDT

14 May 15/

"I believe Ms. Shaw is almost to your position Ms. Groves," Harold cautioned.

Root lurched back as one of Alexi's men took a wild swing at her with his knife. She backed up another step, right into a concrete wall. "I'm occupied at the moment Harry," she said dryly, reaching her hands out cautiously, looking for something to use as a weapon. She always ran out of ammo at the most inopportune moments.

The Russian flashed her a lopsided smile, expertly twirling the combat knife between his fingers. "You're the crazy eyed one," he smirked.

Root felt her lip twitch into a smile of her own. "Well, I've certainly been called worse," she said smoothly.

"Alexi really wants you dead," The Russian sounded almost sorry about that.

"Mm, hate to disappoint," Root grinned hollowly as her fingers finally closed around a thin metal rod.

The Russian smirked at her, and then froze, crumbling in front of her, unconscious or dead, she wasn't sure. Shaw stood behind him, holding a fire extinguisher. Shaw glared up at her and dropped the extinguisher on the Russian for good measure. He groaned, still alive, but clearly not getting up anytime soon.

"Here," Shaw muttered, handing Root her Nano. "Don't lose it," she added angrily. Shaw squatted down and grabbed the Russians knife. She dug it into the strap of the anklet she was still wearing. It dropped to the ground, buzzing angrily every few seconds.

Root nodded and swallowed hard. When Harold had strapped that to her in the library she hadn't been able to make it two feet. Shaw had made it halfway across town. Whatever Shaw was up to, and it was definitely something, she was still trying to protect them. That was something. That could be enough for now. Samaritan hadn't broken her, not entirely. "She's here Harry," she added, a small smile on her lips as she stared at Shaw. She bit back a grimace at the large welt forming along Shaw's jawline. Shaw rolled her eyes.

"Where's Reese?" Shaw asked, adjusting the strap on her M4.

"We got separated, he's on the first floor with the processor," Root bit her lip.

Shaw nodded slowly.

"I'm by the back exit. There's a car here, we can hotwire it," Reese announced. Root sighed in relief.

"He's out back," Root repeated for Shaw.

Without a word Shaw raised her rifle and turned towards the door, guiding them through the building. She dropped everyone in their way, leaving none of them alive. Root watched her warily.

"I hear gunfire coming towards me Root," Reese said, sounding nervous.

"That's us John," Root assured him.

Shaw moved to clear a corner and Root grabbed her, pulling her back. "There's a camera on the far wall," Root whispered. Root leaned out of cover and shot it.

Shaw sighed. "This place is going to be crawling with agents soon," she growled.

Root raised an eyebrow, "Isn't it already?"

Shaw glared up at her, "No," she said simply. Root shook her head in exasperation

When they got to Reese he glared at Shaw but didn't raise his gun. He handed Root the protective briefcase containing the processor and reloaded his pistol, refusing to take his eyes off Shaw.

Shaw sighed as she brushed past him to the yellow Camry in the lot. "Harold's fine," she sighed, smashing the driver's side window with her elbow, "Bear is fine," she added, skimming the car's wires against one another, looking for a spark. "Obviously," she finished, sending them both a glare. The car revved to life and Shaw grinned.

Root slid into the passenger's seat while Reese climbed in the back. Shaw pulled her hood over her eyes and sank low into her chair before gunning the car out of the back alley, right towards two Russians standing watch. Shaw spun the wheel hard, slamming them against the tail of the car before they could raise their guns. Two more Russians saw and jumped in a van to pursue them.

She weaved in and out of traffic effortlessly, but the Russians weren't far behind. They chased them through block after block, using their van to barrel through cars when Shaw outmaneuvered them. Growling, Shaw leaned into the gas harder and merged onto the highway before quickly peeling back off it, skidding to a halt under a bridge.

"This block's on the Shadow Map. There's a parking lot through that alley," She said quickly. Reese nodded and got out of the car. "Get back to Finch."

Root felt a knot growing in her stomach. "Sameen, what are you-"

"Root, we don't have time for this," Shaw hissed.

Root shook her head. This was too familiar. Her chest tightened. "No, no, you aren't doing this again," Root growled. Shaw sighed and leaned across the car, inches from Root's face, her hands braced on Root's seat and the car door. Root backed up against the car door, "I'm not falling for that," she added, glaring at Shaw's lips.

Shaw's mouth twitched. "Didn't think you would," she said, opening the car door behind Root and shoving her out in one fluid motion, leaving her sprawled across the pavement. Root staggered back to her feet but Shaw was already halfway down the block.

"She still has the processor, doesn't she," Reese growled. Root closed her eyes and nodded.

"Let's go," she muttered, ducking into the alley just as the Russian's sped past them, still pursuing the Camry.

Reese had another car ready to go in seconds. Following the Russians and Shaw didn't prove particularly difficult either, since the Russians seemed hell bent on leaving a trail of destruction behind them.

As they neared a bridge, the tail of the Russian's van finally came into view and with it the sound of gunfire. One of the men was leaning out the window, firing an M16 towards Shaw's Camry. Sparks shot out the back of the Camry as both of the back tires blew out. The car spun wildly, slamming into the median with enough force to send the Camry spinning through the opposite lane of traffic and over the guardrail, before plummeting into the river far below.

Reese slammed on the car breaks and Root felt all the air leave her body. Not again. Not like this. The Russians stopped briefly to look down at the wreckage before moving on, content that the job was done.

"John. Please," She whispered, her voice broken.

Reese nodded. "I'm going," he assured her, swinging their car around. Root's vision blurred, her head was spinning, and her breath came in smaller and smaller gasps. "Breathe," Reese ordered, glaring between her and the road as he pulled into the parking lot below the bridge. Root leapt from the car before it was fully stopped, sprinting towards the tail end of the little yellow Camry bopping upside down in the water.

She made it to the dock before hands wrapped around her middle, pulling her off her feet.

"You can't go in there Root," Reese insisted, breathing heavily from exertion.

"No, you can't do this," Root screamed, kicking against him helplessly, "Let go." She couldn't breathe, it was all spinning in front of her now, the kiss, the gunshots, Martine, that damn grate. And now the car was spinning out completely, sailing over traffic and into the water. Root sank to her knees, her chest tightening painfully. This couldn't happen again.

Suddenly a hand broke through the surf at their feet, then a head. Shaw gasped as she came up for air, clawing at the dock with one arm. She staggered to her feet in front of them, a large gash over her right eye, her teeth chattering. Glaring, she stalked over to them, roughly shoving the case that held the processor into Reese's chest.

"Hope that was waterproof," she muttered, not bothering to look at either of them as she brushed past them.

* * *

 _Thanks you to my beta witheveryheartbeat/broodystars (Ao3/tumblr) and to everyone whose sticking with this story and commenting on it, its awesome to hear from you all! 01/11/16_


	13. Needles and Threads

_I am so so sorry everyone. I uh...no real excuse...I got hooked on the 1OO and clexa happened and then well...I've had a hard time reorienting to focus back on this._

 _That said, this fic had a finished rough draft months ago, and me uploading shit is just a matter of me refocusing so I can properly edit the ending. So to everyone still willing to stick with this fic, it WILL be finished. I promise. You aren't committed or attached to a fic thats not getting an ending._

 _Anyways, thank you to anyone/everyone who chooses to stick with this and to all the ppl who've messaged me expressing their desire to see this continued. And as always thank you to my beta reader broodystars._

* * *

/Location: New York: Below Ground

40°42'50.1"N 73°59'53.9"W

1100 EDT

14 May 15/

"Oh, thank goodness," Harold's shoulders visibly sagged with relief as they entered the subway.

Root nodded numbly as he continued babbling. She watched as Shaw moved slowly to the train car, quietly analyzing the deep cut over her eye in the train car's reflection; she was still shivering. Shaw moved slowly, her left arm tucked across her stomach to keep it from moving too much. Her lips were pursed and her jaw tight. Root looked at her and felt her throat tighten.

"That needs stitches," Root said quietly, gesturing to Shaw's head.

Shaw shrugged. Rolling her eyes, Root walked over to Shaw's side. She didn't have Shaw's medical experience, but she knew without a doubt that the cut above Shaw's eye needed attention. Root gently took her good arm and dragged her into the subway car. She steered her to a seat and pulled out the medical kit.

Shaw stared at the ceiling, not blinking while Root worked. Root hadn't done this often, especially not to someone's face, but it'd have to do. Root bit her lip as she finished the stitch and grabbed Shaw's chin, gently turning the woman to look at her so she could see the stitches from a different angle.

"It shouldn't scar," she said quietly, hoping she sounded more sure than she was. "But you'll still look good if it does," she smiled lightly, trying to get any reaction from Shaw. Shaw blinked and looked away.

Root felt her throat tighten painfully and her stomach dropped. Shaw wasn't silent with her anger, she was a force of nature; wild, uncontrollable, and never delicate. The woman in front of her was a statue. Root didn't know what to do with this Shaw.

Harold and Reese approached the car slowly, hovering in the doorway.

"The processor appears to be intact Ms. Groves," Harold said slowly, glancing between her and Shaw nervously.

"So what now?" Reese asked quietly, starring at Shaw.

"I can make some calls. Manufacturers who can replicate this processor for us. Without Samaritan seeing, if we're fortunate," Harold explained.

"You won't be," Shaw muttered, her jaw clenched.

Harold raised an eyebrow. "Please enlighten us Ms. Shaw?" he said dryly.

Root glared at him. "She saved both of us back there Harold," she reminded him.

Harold pursed his lips. "Or perhaps this is all part of some elaborate long-con Ms. Groves. I sincerely hope not, but unless Ms. Shaw cares to be more forthcoming about her …allegiance, well, I don't see what choice we have."

"If you're lucky, Samaritan thinks both of you were in that car," Shaw said quietly, her voice cold. Root frowned. "Within 24 hours the river will be dragged and when no bodies show up, all three of you will be back at the top of Samaritans list." Root's throated tightened as a nauseating thought struck her; had Sameen thrown the car off the bridge on purpose? "They'll put everyone they can on the hunt for you and for The Machine," Shaw finally blinked and tilted her head slightly to look at Harold. "The only leverage you had here Finch was that Greer didn't know for sure that The Machine was gone."

"And now they knows She's alive," Root said quietly.

"Yes," Shaw said coolly. "Or, at the very least that you're looking to rebuild," she shrugged, "Either way…"

"So what do you suggest we do Ms. Shaw?" Harold asked skeptically.

Shaw blinked, her shoulder's tensing, and she looked up at him, fury in her eyes. "You run," she hissed.

Harold nodded slowly as he considered her words. "I'm afraid we can't do that," he said sadly.

Root glanced up at him in surprise. He'd been ready to hide for eternity when Samaritan had been turned on. As if sensing her confusion Harold turned to her, "We wouldn't make it far even if we did. When Ms. Shaw executed Mr. Elias and his associate she demonstrated how Samaritan chooses to deal with retreating opponents."

"I can get you out of the city," Shaw said finally. "You'll need to go further…Montana, Cuba, somewhere else entirely…just," she clenched her jaw, "Somewhere else. Somewhere I don't know."

Reese nodded slowly. "This is cyberwarfare Finch. We could rebuild The Machine from anywhere…uh, couldn't we?"

Root frowned, a wave of anxiety washing over her, "And what about you?" She turned to Shaw, staring at her intently, willing the other woman to look at her.

Shaw blinked but kept staring straight ahead. "New assignment," she shrugged. "Probably."

"Probably? As in, assuming they don't kill you," Root scoffed.

Shaw shrugged again.

Root grit her teeth, feeling a wave of anger course through her at Shaw's nonchalance. "No, Sam that's not good enough."

Shaw rolled her eyes, her fists tightening almost imperceptibly at her sides. It was enough for Root. She put her hands on Shaw's knees and squatted in front of Shaw, determined to get her attention.

"This doesn't make sense," Root said quietly, her voice strained. "Just tell us, tell me, what's going on?" There had to be an explanation for all of it. Shaw wouldn't just hand them over to Samaritan, she wouldn't murder Fusco…she wouldn't. But why she refused to be forthcoming, Root couldn't understand. "You wouldn't…"

Shaw's lip twitched and her eyes snapped to Root's, glaring at her furiously. Shaw licked her lip. "I did Root. I gave you up. I told them all about the implant and how you talk to The Machine." Shaw's lip curled angrily and she leaned towards Root until they were only inches apart. "So stop trying to protect me," she hissed.

Blinking back tears, Root stood and stepped away from Shaw. She wasn't giving up. She wouldn't ever do that. But Shaw wasn't herself right now and Root had no idea how to get through to this stony version of Shaw.

"If you really did that Ms. Shaw, in addition to whatever you've done to Detective Fusco, why should we trust you to lead us out of town?" Harold whispered.

"You could lead us straight to Samaritan and we'd be sitting ducks," Reese added, his voice low.

Shaw's jaw clenched, "And what exactly are you now John?" she challenged.

Reese stared at her angrily. "Just tell us where Fusco is Shaw," he growled.

"He's safe," she sighed. "Safer than you actually," she added, almost to herself.

Reese shook his head, "This games getting old," he warned.

"Then waste your precious lead time torturing me for information," Shaw challenged, "Doesn't change much for me." She stood then, slowly, still cradling her injured arm. "Fusco is safest being as far away from the three of you as possible. You all can cut and run. He has a son." She glared at them angrily. "You can't help him," she said the words slowly, staring intensely at Reese.

"We should do what she says," Root said quietly, folding her arms across her chest. "If this last week has been Samaritans idea of cease fire then we definitely just broke it."

"I'm not sure I see a viable alternative," Harold admitted begrudgingly.

Reese glared at both of them angrily, like he wanted to argue, but he said nothing.

Shaw nodded slowly. "Good," she sighed and stood to leave the train car. "Don't forget to pack something to eat," she muttered as she brushed past Reese.

/Location: New Jersey: Kline Hotel

40°29'42.4"N 74°17'48.0"W

1800 EDT

14 May 15/

Root was no stranger to bad motels. Between her time as a runaway, her work as an assassin, and her work for The Machine, bad motels were a pretty standard experience. But this place was bad. The smell alone was, well, dwelling on it was probably a bad idea. She bit down a gag and turned to watch Shaw. Shaw seemed completely unfazed by the room, plopping down on the side of the bed with a sigh. Root raised an eyebrow as she realized there was only one bed in the room and bit back a grin at the thought of Reese and Harold being forced to share the same accommodations next door.

Sighing, she set her bag on the ground gently, mindful of the syringes full of sedatives she'd thrown in at the last minute, and rolled her shoulders. Harold had taken so many precautions to lock down the subway they'd barely made it out of the city before Shaw had pulled over at this crap hole, insisting they couldn't safely get any further that evening.

"Well this is cozy," Root said playfully, still trying to draw a real reaction out of the other woman. Shaw said nothing and Root grit her teeth. This ended now. "You need to talk to me Sameen," she said slowly, struggling to keep her voice level and commanding.

Shaw didn't respond.

Root nodded slowly, feeling her composure slipping away completely. "Well you can listen then," Root stormed over to Shaw, leaning down so she was inches away from Shaw's face. "I know you. I know you wouldn't just give any of us up to Samaritan," Shaw's jaw clenched involuntarily and Root felt a small rush of confidence, knowing that her presence was affecting Shaw, even if she desperately didn't want to show it. "We looked for you," she promised and Shaw flinched. "I'm not losing you again," Root swallowed hard. She bit her lip, debating if she should continue. "I care about you Sam and I-"

"Stop," Shaw sneered.

Root grit her teeth and let out a shaky breathe. "I'm not letting you-"

"Not letting me?" A smirk twisted across Shaw's lips and she raised her head to meet Root's eyes. The smirk slid away quickly and she shook her head. "At the stock exchange…it had to be me. You know that Root. In that moment…" she watched Shaw struggle for the right word and then sigh, defeated. She shrugged, "I was expendable."

"That's never been true, Sameen, not for a second," Root grit her teeth as she pulled back.

Shaw stared at her for a moment and then nodded slowly. Her fists clenched against the ratty bed spread and she sighed in exhaustion, "Root…" she muttered sadly. A hand reached out slowly, resting lightly on Root's hip. Root blinked in surprise as Shaw tugged her closer, resting her forehead against Root's stomach. Root's throat tightened and she stopped breathing, tentatively reaching out to run a hand through Shaw's hair. She gasped suddenly as she felt a needle slide into her hip. "It still is," Shaw explained, looking up at her with a haunted look in her eyes.

The room started to spin, "Sameen…" Root plead, buckling to her knees. "Don't…"

Shaw caught her, cradling Root as the drug took hold. Root blinked rapidly, everything was going dark around the edges. Root squinted, fighting against the darkness as Shaw's lips started to move again, but the words were too fuzzy, too distant to make out and everything went black.

* * *

 _One last thing I did want to add...This fic was written/finished in like...oh god its been so long. Like December (yikes). Um...before all this year of tv turned into such an epic disaster. That said...while it will be a potentially anxiety inducing ride through this fic...I'm not personally big on multi-chapter fanfics which 'surprise' you by actually killing half your pairing (Or, as it turns out, TV shows). So...there are a few chapters where it might not look good but there will be no code 307's and any chapters that end in a 'oh gosh will they live!?' fashion are going to be updated 100000 times quicker than this update was b/c I won't leave you hanging with that either. Maybe that spoils the suspense for some people but I think the PoI and the 1OO fandom crossover a decent bit and I think we've all been through enough. -4/17/2016_


	14. Bad Odds

_I'm super excited for tomorrow as I'm sure all of you are! Thank you to everyone who stuck with the fic, I'm so glad that there are still people interested :) And as always, thank you to my beta witheveryheartbeat/broodystars (here/tumblr)._

* * *

/Location: New Jersey: Kline Hotel

40°29'42.4"N 74°17'48.0"W

2025 EDT

14 May 15/

Root awoke to something wet on her skin. She blinked slowly, and turned to look at her hand. Bear sat next to her, and when he realized she was awake he made a low whining noise.

"Oh good, you're awake Ms. Groves," Harold sighed with relief. Reese nodded once, in acknowledgement, before turning back to the window. He held his gun by his hip.

As the events from earlier slowly trickled back to her, Root bolted up right, ignoring the way the room still spun.

"Easy, easy," Harold cautioned as he came to her side offering her a glass of water.

"She drugged me," Root whispered, her voice cracking.

"Ms. Shaw drugged both of us," Harold said bitterly. "And she took The Machine."

"What?" Root leaned forward on the bed, pressing the heel of her palm against her forehead. "I don't understand," she shook her head as her voice cracked.

"It seems pretty straight forward Root," Reese said quietly.

"Indeed," Harold sighed. "Ms. Shaw shot at Mr. Reese on her way out."

Root shook her head frantically, "No I…there has to be some explanation," she turned to Harold, her eyes large and pleading.

He put his hand on her shoulder sympathetically. "I think Sameen has made her allegiance very clear," he said gently.

"After I checked on you and Finch, I went back out to look for Shaw. There was blood in the parking lot. I clipped her I guess, don't know how badly. But she's definitely injured," Reese assured them.

Root bit into her lip to stop it from quivering. "She said…before she left she said she was going back to save us," Root shook her head.

"By giving The Machine to Samaritan?" Harold pursed his lips. "Perhaps…in some way, she does believe that Ms. Groves," he conceded, "However, I think we can agree that Ms. Shaw is not truly acting in our best interests at this point," he added delicately. His phone began to vibrate madly, and he pulled it out, a grim expression on his face. "The security alarms at the subway have just been triggered," he glanced between them sadly, "I believe Ms. Shaw has informed her superiors about our base of operations."

He clicked a few buttons on his phone and nodded to himself, before handing the phone to Root. Security footage from a hidden camera inside the subway was playing. Two dozen Samaritan agents, all heavily armed and led by Jeremy Lambert, were tossing the place inside out. Feeling ill and unable to watch any longer, Root handed the phone to Reese.

"How do you want to handle this Finch?" Reese asked.

"We cannot allow The Machine to be destroyed," Harold said gravely.

Root nodded in agreement. "So we follow Sameen," she said quietly.

"I bugged her Nano. It shouldn't be a problem," Reese sighed.

Root grimaced, "You mean this Nano?" she pulled the gun from the waistband of her jeans.

Reese growled.

"Any other ideas," Finch sighed.

"Alexi," Root said finally. "He's her asset," she said the words bitterly. "He's worked with Lambert too. Maybe he knows something," she sighed.

"I don't think we have any other leads," Harold admitted. "Alexi hosts illicit poker games every week…" he looked at his watch, "If we hurry, we can make it back to the city before it ends."

"We'll need more guns," Root said, thinking back to their disastrous fight at Quantum Dynamics.

"Elias's bunker. Shaw never knew about that, those guns are safe," Reese grinned.

Root flinched. "Except she does know," she corrected, her voice small.

"Damnit Root," he sighed.

"That is…certainly interesting news," Harold said slowly, his sentence fragmented as he struggled with his next thought, "I installed security at the bunker that is identical to the subway's security. But that alarm has not gone off," he finished.

Root exhaled slowly, "So maybe it's still safe."

Reese glared at her angrily. "We'll see," he said spitefully.

She grit her teeth, biting back a dozen retorts. "Do you want to say something John?" she asked icily, an angry smirk on her face as she turned to him.

Reese leaned forward. "We don't know what we're going to be walking into Root. I need to know you won't pull a gun on me again."

Her jaw clenched. "Then don't threaten Shaw again," Root glared up at him defiantly.

They glared at each other angrily, without blinking, without breathing until Harold sighed heavily. "Perhaps, we should find Alexi first. And devise a plan of…containment for Ms. Shaw once we have a better idea of where she is," he offered diplomatically.

/Location: New York

40°47'42.0"N 73°56'40.5"W

2315 EDT

14 May 15/

"In position," Reese said warily.

Root nodded and pressed her finger to her ear. "I'm ready," she announced, racking the slide of her shotgun with her other hand. Shotguns weren't her usual, but she didn't see a good reason to let Elias's extensive arsenal go to waste. Her two pistols were tucked into the waistband of her jeans, with a back-up piece strapped to each ankle. There was also a duffle bag full of assault rifles in the car with Harold up the block. She shifted uncomfortably, pulling at the edge of the bulletproof vest she was wearing. They would not be underestimating Alexi's extensive firepower again.

She faintly heard the sound of a window breaking on the other side of the restaurant and smoke slowly drifted out of the building. She grinned; that was her cue. A few patrons barged out of the place, falling to their knees, gasping. Root pulled out one pistol, kneecapping each of them for good measure. She pulled her gas mask down and moved in. Everyone in the front room was already unconscious.

She could hear gunfire coming from the alley to her left, where Reese was. A Russian barged through from the kitchen and Root dropped him before he even saw her. She moved towards the kitchen entrance and kicked the swinging door open but didn't go in. Bullets riddled the door and Root waited until she heard the click of an empty mag. She burst through the door, pumping the shotgun twice, hitting one man in the chest and a second in the leg. In the metallic reflection of the pots and pans she saw movement and spun quickly, as a Russian swung at her with a knife. She blocked the swing with the side of the shotgun and smirked. It was the same man who had cornered her in Quantum Dynamics.

"Well you certainly like your knives," Root grinned.

He returned her smile. "It's more intimate," he admitted, his grin widening. He swung again and Root backed up, turning the shotgun on him, but it clicked hollowly. She rolled her eyes as she ducked around the corner to avoid the man's wild swing, feeling the blade burn as it grazed her shoulder. Root grimaced. This was why she didn't like shotguns. Too much reloading and it left you exposed. She pulled her pistol from behind her back and put a bullet into each of his legs. He whimpered as he went down.

Root paused to reload before exiting back into the front room. Reese was waiting for her by another door. "You ok?" she gestured to his blood covered arm and Reese shrugged.

She joined him, standing across the door from him. "Ready?" he asked, pulling the corner shot grenade launcher from off his back.

She nodded and cracked the door open, firing blindly into the room to give Reese cover while he fired the launcher around the bend of the door.

Cries went up throughout the room as the Russians dove for cover. Root waited for Reese's signal and then spun and walked through the door, shotgunning two men who still had their pistols drawn. Reese took out another three across the room.

She moved forward deliberately, her eyes on the man on the ground in front of her. Alexi. He was struggling to get to his feet, his gun in hand.

She leveled the shotgun against his head, "I wouldn't," she threatened. He turned his head slowly to glare at her and dropped his gun. Reese joined her, grabbing Alexi roughly by the collar of his shirt and slamming him into a chair. She handed Reese a zip tie and he yanked Alexi's arms behind his back.

"Let's do the others," Reese ordered. She handed him some more zip ties and walked around the room, cuffing anyone still breathing. They returned to Alexi a moment later.

He stared at them furiously. "The crazy eyed one and the urban legend. That bitch was supposed to keep you out of my business," he huffed.

Root's hands clenched.

"Where is she?" Reese asked, his eyes menacing despite the lightness in his tone. Alexi laughed, and Reese sighed in irritation. "Well that's rude. I asked nicely," Reese growled, snapping Alexi's finger.

Alexi grimaced, baring his teeth at them. He sighed and chuckled again. "The smoke is clearing," he said evenly.

Root blinked, cocking her head in confusion.

"Your observation skills are impressive," Reese muttered, his voice gravely.

Alexi smirked openly. "You'll be able to see the cameras then," he explained.

Root's heart stopped and she stared at the nearest wall, where she could just make out the red blinking of a light. She dropped her shotgun and pulled her pistol, shooting out the eye.

"That was not wise," Alexi told her, still grinning. Shaw's warning about Samaritan Trigger Teams response time echoed in Root's head and she tightened her grip on her gun. Root's eyes traveled around the room. There was a camera on every wall and the smoke was almost completely gone.

"Samaritan likes having eyes on its people," Alexi added, his voice suddenly grave. "Just in case."

Root's eyes widened in alarm. "No," she spun back to Alexi just as he started seizing violently.

"Get him on the ground," Reese yelled, cutting the zip tie holding Alexi upright. Around the room, the other men began to convulse. Alexi kept seizing until he gave one final jerk and went still.

Root leaned down numbly, knowing what she'd find. "He's dead," she glanced around the room at all the others who had stopped moving too.

Reese pursed his lips. "Well, at least we know Shaw wasn't lying about something," he said grimly.

Root glared at him angrily and he shrugged. They walked back through the building, not at all surprised to find that the men in the kitchen were both dead too.

Harold was waiting for them outside. "Any news?" he asked hopefully.

Root shook her head.

"Samaritan killed them," Reese muttered. "Shaw was right about the implants."

"That's very troubling news indeed Mr. Reese," Harold sighed. "Did you at least find something useful before…"

Sighing, Root shook her head again. They had nothing, and with every minute that passed the odds of Shaw and The Machine being dead increased tenfold.

Reese's phone rang suddenly, startling her from her thoughts. Reese's brow furrowed. "It's Fusco's number," he said nervously, putting the phone on speaker.

"Hey Wonder Boy, I was told to give you an address," Fusco said, not sounding remotely distressed.

"Lionel, where are you?" Reese asked, clearly relieved to finally hear his partner's voice.

"That's what I'm trying to tell you. You got a pen?" Fusco retorted.

"Did someone order you to do this Detective?" Harold chimed in.

"Yeah, Shaw said you would need this," Fusco paused. "Also said you probably wouldn't be happy to hear that. Which makes sense. She's been a bit more uh, trigger happy than normal since she got back," he added calmly.

All three of them exchanged looks.

"This seems…questionable," Harold said slowly.

"Lionel, are you being held against your will?" Reese asked evenly.

"Eh, I'm not exactly free to go but I'm not in a hurry to either. Shaw won't read me in but uh, I'm pretty sure you're gonna wanna get over here Reese," Fusco said seriously. "I think she's about to do something stupid. Like at the Stock Exchange."

* * *

 _Thank you again for reading/reviewing :) -5/02/2016_


	15. 90 Seconds

_As always thank you to my beta broodystars :)_

* * *

/Location: New Jersey: Kline Hotel

40°29'42.4"N 74°17'48.0"W

1830 EDT

14 May 15/

The cocking of a gun paused Shaw in her tracks. "Where you going Shaw?" Reese asked lightly. Shaw clenched her jaw and turned to him slowly, raising her hands into the air, not letting go of the briefcase containing The Machine. Reese kept his silenced pistol trained on her but didn't move forward.

"Just let me walk away John," she said quietly.

"Not while you're holding that briefcase," he said, his voice losing all hints of levity.

She nodded slowly, her eyes scanning the parking lot. "I kinda need it," she smirked.

Reese shook his head, "I'm really running out of reasons not to shoot you Shaw," he admitted sadly.

"That's unfortunate," she agreed, taking a step backwards.

Reese straightened his arm, raising his gun from his hip to his shoulder. "Don't do that again." He grit his teeth and sighed. "If this isn't what it looks like then tell me. Last chance," he warned.

She cocked her head slightly, her lips pressed together into a thin line. "Right after we met you said something to me," she inhaled deeply, keeping her eyes trained on the gun, "That in this line of work we're walking in the dark," she said.

Reese nodded and cocked his head to the side, "But we don't have to walk in it alone. I remember," he furrowed his brow, looking for some indication of where this was going.

"We weren't in the dark John," Shaw said quietly, "Not with Finch."

Reese narrowed his eyes in realization, "But you are now."

She stared at him for a long moment, the rush of traffic on the nearby overpass near deafening in the silence. "Yes."

Reese's eyes hardened and he opened fire, sending Shaw diving for cover behind a Ford truck. She hissed as she felt a bullet graze her calf and bit back a smirk. Reese was still going for her knees. That was surprisingly generous of him.

Shaw screwed her silencer onto her gun and shot blindly around the corner of the truck, aiming wide of where she knew Reese was. She inched her way down the side of the truck, her calf burning with every crouched step. She popped up at the other end of the car, firing wide of Reese again, but pushing him further back. He fired again and the car window above her shattered. The safety glass rained down on her and she cursed as she brushed it off of her. Reaching her hand up through the broken window she popped the door open and grabbed the wires under the car, quickly bringing the car to life. She tossed the briefcase into the passenger's seat and crawled in. Shaw slammed her uninjured foot on the accelerator and sped out of the parking lot.

She didn't dare go to the highways right away, instead she wove in and out of side streets until she was sure she was alone. Pulling over in a dark alley behind a local bar she ripped the sleeve of her shirt into a makeshift tourniquet for her leg. It wasn't pretty, and she'd lost some blood leaving it untreated that long. She sighed. Not that it particularly mattered. Fishing her hand into her pocket she pulled out her cellphone. As she dialed blood smeared across the screen.

"Hello?" Fusco sounded irritated. He'd probably been asleep.

Shaw rolled her eyes. "Hate to interrupt your beauty sleep Lionel, but we're meeting."

"Now?" he sighed.

"A few hours," Shaw closed her eyes. "Don't forget the duffel bag," she listened to the rustle of sheets as Fusco muttered to himself, "And Fusco, be careful with the gas." He started swearing as she cut the line.

/Location: New York: Manhattan

40°45'46.4"N 73°58'43.9"W

2330 EDT

14 May 15/

Shaw bit the inside of her cheek to keep from limping. As she entered the lobby her eyes darted around nervously, assessing all the cameras in the room. She moved around the perimeter, never giving a camera a clear view of her face.

Fusco and Claire were seated at the bar, both looking anxious. Shaw rolled her eyes. Amateurs.

She slid the briefcase onto the table and Claire's eyes widened. "How could it possibly fit…"

Shaw shook her head, "Don't know. Don't care either," she flagged down a bartender. "Whiskey, double."

"You look like death Shaw," Fusco said, watching her with concern in his eyes.

Shaw took her drink and downed it, closing her eyes as it burned through her throat. That'd take the edge off her leg. "I'll be fine," she glared at him, daring him to argue. She grabbed the duffle bag that was stretched across the barstool next to him and turned to Claire. "You have the flash drives?"

The girl nodded nervously, brushing her brunette hair out of her eyes. She pulled two flash drives out of her pocket, one red, one blue. A Matrix reference. Shaw rolled her eyes. Why did she know that? She pursed her lips as Claire looked at her sheepishly.

"If this is the last thing I'm gonna do, I might as well enjoy it," the young girl said, a slightly bitter smile crossing her lips.

Shaw tilted her head, her eyes narrowing. "It's way too late for cold feet Mahoney."

Claire returned her glare. "I'm not afraid."

Shaw nodded.

"You gonna read me in on this Shaw?" Fusco grumbled.

Shaw glared down at her empty glass and sighed. "It's better this way. Trust me." She exhaled heavily and dug a bulletproof vest from the bag. She secured it around her chest before throwing a coat on over it.

Fusco stared at her for a long moment, clearly not convinced.

"Your friends'…stunt at Quantum Dynamics this morning really messed things up," Claire said suddenly. "Greer pulled every active unit in the region back to New York."

"Figured it would," Shaw nodded. "I got them out of town, gave Greer a location- old base of operations they used. Should pull a dozen or so off base."

"For how long?" Claire asked skeptically.

Shaw shrugged. "Well, if the bomb works, permanently."

Fusco cringed. "Ah, I wish you hadn't said that," he muttered.

Shaw grinned bitterly, "Still wanna be read in Lionel?"

"Yes," he glared back at her. She shrugged.

"Well, I better be going," Shaw grabbed the flashdrive Claire handed her and slid the briefcase over to her. "She doesn't leave the room," Shaw ordered, pointing at Claire. "But don't let them shoot her either," she added. "Reese might want to."

"Still don't trust me Shaw?" Claire narrowed her eyes.

Shaw shrugged, "It'd be real easy to back out now."

Claire blinked at her icily. "I know why I'm here," she said, her voice low and angry.

Nodding slowly, Shaw turned to Fusco. "Call at midnight."

"Sure thing…uh," Fusco shifted nervously.

"What Lionel?"

"Anything you want me to say? You know, to tall, dark, and crazy," he asked, staring at her intensely.

She stiffened, her jaw clenching involuntarily. She considered her answer carefully. "Doubt there's much I could say at this point that'd make a difference."

Fusco smirked. "I'll make up something good then. Keep her from being too angry at you when you get back."

Shaw rolled her eyes, feeling a burning tightness in her throat that probably wasn't the whiskey. "Yeah, you do that," she muttered, heading for the door.

"Shaw," Claire called after her. "Remember. 90 seconds. That's all you get."

"I know," Shaw sighed.

Shaw exited the building and stared up at the building across from her. Samaritan Headquarters. Right here, in the heart of Manhattan. She grit her teeth and crossed the street, careful not to limp even a little bit. Swiping her ID as she entered the lobby and moved down a long hallway until she was at the staircase.

She leaned against a wall and casually checked her phone. Midnight was moments away. She inhaled deeply, closing her eyes, counting down in her head. 3...2…1.

90 Seconds.

She opened her eyes. It was time to end this.

Yanking open the door, she pulled a gas mask from the duffle and took the stairs two at a time. At the base of the stairs she checked her watch. 65 seconds to go. She grit her teeth and sprinted down the hallway. The sound of her running echoed in the empty corridor, alerting two guards who popped out from behind cover with their weapons drawn. Shaw slid to her knees, taking both out before they could fire. She staggered back to her feet, hissing at the pain in her calf.

The sound of their bodies dropping pulled more guards out of the nearby security station. Shaw rolled behind cover, pulling a grenade from the duffle. She threw it towards them and closed her eyes, wincing as the flashbang went off. Surging forward, she twisted her body over one guard's back, slamming him into the ground and dropped the other two with a few quick strikes. She glanced at the security monitors in the room. She was featured on at least 6 and there were easily two dozen agents headed her way. Her eyes moved to her watch. Thirty six seconds. Grabbing one guard's access key she kept moving.

She rushed towards the giant double doors at the end of the hallway and swiped the guard's key. Pushing through the doors, she sucked in a breath.

Before Samaritan had fully come online, Root had shown her the belly of the beast. A Samaritan server farm. Just one limb of the beast, an arm or a leg. It was the raw processing power of Samaritan that was housed in warehouses like that. But this, this was the beasts brain. It's true brain. These servers controlled all the others. Samaritan started here. In this room.

Honestly, she'd expected it to be bigger.

The room was barely twenty by twenty. Servers lined the walls and cables were threaded and criss-crossed across the floor and ceiling. A single computer screen and keyboard sat in the center.

Shaw limped forward, and turned the monitor on. As it booted up Shaw inserted the flash drive. She closed her eyes, forcing herself to remember the command code Claire had written. She punched it in slowly and hit enter. The screen went black.

Shaw frowned and glanced at her watch. Only 10 seconds left.

She pushed a hand to her ear. "Claire, the screen just went black." Guards were pounding on the door outside. Shaw fished a dial out of her bag and cranked it up all the way.

"That's supposed to happen," Claire assured her, "I think."

"You think?" Shaw hissed. "If this goes pear shaped we don't get a do over," she added, barely able to contain her fury. The pounding on the door stopped.

"There isn't exactly a manual on how to do this…" Claire snarked, her voice cracking. "Either way, we'll know in a moment."

Inhaling deeply, Shaw nodded and begun to countdown. 3…2…1

"Well?"

"Give it a second," Claire sighed. Shaw could hear Claire clicking away on her computer. "Just got three reports of power outages around the city. Rolling blackouts have started," Claire swallowed hard. "It worked," she said, her voice weak. "The virus is in."

Shaw sighed, glancing around the room. "How long do we have?"

"I don't know entirely. Samaritan will syphon power to keep itself going, so it'll be a little bit. But not long…maybe an hour?" Claire's voice was breaking.

Shaw rolled her eyes. "It's really too late for cold feet now Mahoney," she said darkly, a small smirk on her lips.

"Heh, yeah, guess so," Claire was crying, Shaw could tell. "You coming back? One last celebratory drink?"

"Maybe," Shaw pursed her lips. "Have a few things I need to do here first."

"Ok," Claire's voice was small, like a kid's. Shaw sighed. Claire was just a kid really. "Normally I'd say be safe or something but…"

Shaw smirked. "Yeah, save it." She nodded her head slowly. "Enjoy your drink," she added, tapping her ear to end the call.

She pulled her gas mask down over her face and opened the doors. Nearly two dozen guards lay strewn in the hallway, still hazy with fumes, all unconscious. Shaw smirked. "Nice work with the gas Mahoney," she muttered.

Shaw limped back down the hallway, past the rest of the unconscious and dead guards. She went to the elevator and paused. With rolling blackouts it'd probably be best to take the stairs. She grimaced and headed back to the stairs, getting to the 13th floor as quickly as she could.

The guard blinked in surprise when she flung open the door to the 13th floor and Shaw hit him over the head with the butt of her gun and kicked him again for good measure. She moved down the hallway quietly, feeling blood begin to leak down her calf.

Finding the right cell didn't prove difficult. The two guards stationed outside were the only security in sight. Shaw brought them down quickly and opened the door.

Control leapt off the cot to her feet. Her eyes narrowed in surprise.

"Ma'am," Shaw greeted curtly.

Control laughed. "Well this is certainly a surprise," she said angrily.

Shaw shrugged.

"A few months ago, your little friends used a damn rocket to drive me off the road, kidnapped me, and then interrogated me. All because they wanted to know where you were," Control crossed her arms.

"Sounds like I missed a party."

"They were convinced you were being held against your will," Control's eyes drifted up and down her body and she raised an eyebrow. "You don't look like much of a prisoner," she sneered.

Shaw smirked. "You wanna stand here and swap stories about Samaritan's hospitality? You have a bed. That's downright cozy in my book," she glared at the older woman.

"What game is it you're playing here Shaw?" Control asked, taking a step towards Shaw.

"No games. While I'd personally love it if you were stuck here long enough for Lambert to perform a stapedectomy on you without anesthesia," Shaw's lip curled in distaste, "If you're against Samaritan, the place for you is out there, not in here."

A small, knowing smile twitched at the corner of her lips, "I'm sure your girlfriend appreciates your pragmatism."

Shaw glared at her "Don't push it," she hissed.

Control nodded and brushed past Shaw to the door. Shaw sighed and turned to follow. Control had a gun trained on her. Shaw rolled her eyes and raised her hands.

"Not checking the guards?" Control challenged. "We trained you better than that," she shook her head.

"Hersh did," Shaw agreed. The lights flickered and then went off.

"And why exactly should I keep you alive Agent Shaw?" Control growled.

Shaw shrugged. "It doesn't matter much to me either way," she admitted, grinning bitterly. "But if you wanna get out of here, you might want to save the bullet," she smirked. Control paused, lowering the gun slightly.

"And where exactly am I supposed to go?" Control asked, "Greer, Decima, whatever they want to call themselves now, they're terrorists. And Samaritan will find me again, even if I do get out."

"It's being handled," Shaw said simply. The lights flickered back on.

"That's not an answer."

Shaw sighed. "You can interrogate me or you can get back to your daughter, ma'am." Control glared at her and Shaw shrugged. "My girlfriend told me," she added with a sneer.

Control nodded "Give me your vest," she ordered, waving her gun once. Shaw rolled her eyes and peeled her vest off. She tossed it to Control who awkwardly worked her way into it while keeping her gun trained on Shaw. "When I come back, it'll be with a full tactical squad. We'll rain hell down on anyone still here, and I will bring Samaritan back under the control of the ISA. Don't be here." Control spun on her heel and left.

With a sigh, Shaw sank down onto the cot and inhaled deeply. The lights flickered off again. She tightened the bandage around her calf, wiping the blood off on the thighs of her pants. The wound burned more after pushing it up thirteen flights of stairs. She stood back up shakily.

As the lights came back on, Shaw limped down the hallway to the elevator. Fuck the rolling blackouts, she wasn't climbing to the 40th floor.

When she got out of the elevator it was to an empty room. The large projector where Samaritan's commands usually appeared was flickering on and off, the word S.O.S stuck on the screen. She raised her gun.

"I assume this was your doing Ms. Shaw?" Greer's voice drifted to her ears and Shaw wheeled around.

Greer had a gun pointed at her. A Walther PPK it looked like.

"Partly," she admitted, unable to keep the smugness out of her voice.

Greer nodded slowly. "Yes. Partly. You're a self-described hammer Sameen...you certainly aren't the brains behind something so…intricate," he stared at her with disdain. "As usual, you're just a pawn in a larger game you don't understand. An expendable soldier."

Shaw bit back a grin. "But I won, so what does that make you?"

"Unemployed I suppose," he said dryly. "If you came here to gloat-"

"I didn't," Shaw assured him.

Greer tilted his head slowly. "You are aware that you've already signed both of our death warrants?" he asked, raising an eyebrow.

Shaw shrugged. "Sure. But I made you a promise." She fired as Greer did.

She smiled as she watched him crumble to the floor, a bullet between his eyes. She stared at him intensely, almost not believing it was true, that he was finally dead. Her throat tightened and she felt a weight lift off her shoulders. She let out a ragged gasp, an unusual tightness in her chest. As she inhaled, she winced. Her stomach burned. She frowned as the burning feeling grew, becoming overwhelming. Shaw put her hand on her stomach and felt the slickness of blood on her skin and grimaced.

So Greer hadn't missed. She stumbled back to the elevator, her hand smearing blood across the buttons.

Shaw's legs buckled and she swore to herself as she fell against the back of the elevator. Gut shots were the worst. She closed her eyes and inhaled deeply. Greer was dead. Samaritan was dying. She felt a small smile on the corner of her lips as her eyes drifted closed. Mission accomplished.

* * *

 _New episode tonight! - 5/16/2016_


	16. Istanbul

_Hey everyone...the episode airs in 20 minutes and the spoilers I'm hearing are...yikes. So um, if the things I'm hearing prove to be true, I've talked with my beta, broodystars on tumblr, and I'm just not gonna send her the next few chaps, and I'll post them once a day throughout the week to finish this story up._

* * *

/Location: New York: Manhattan

40°45'46.4"N 73°58'43.9"W

0015 EDT

15 May 15/

"Room 802, here," Reese said, pulling his gun from his pocket.

Root nodded, pulling her own guns as Reese knocked. The door opened an inch, the chain still on. Fusco's eyes peered out from the crack and he sighed in relief.

"About time," he grumbled, letting them in. "Shaw's gone who knows where, the power's going on and off, and the other one is just crying on the couch," he said angrily, waving his left arm wildly. His right was in a sling.

"The other one?" Root asked, glancing around the hotel suite nervously. It was a nice room, two beds, large windows, and very clean. The exact opposite of the motel in Jersey. There was an impressive computer station at the desk, which rivaled Harold's setup in the subway.

"Me," a tiny voice said from the door to the bathroom.

Root spun and raised her gun. "Well this is an unpleasant twist," Root smirked down at the smaller woman.

"Claire?" Harold cocked his head.

"You all know each other?" Fusco asked, his eyes wide.

Despite her tear stained cheeks, Claire smiled slightly, raising her hands in surrender. "I know me being here is probably confusing…"

"Not really. Shaw's Samaritan, you're Samaritan," Reese shrugged.

Claire's smile faltered. "Shaw was never Samaritan. Not really. She never believed," Claire's eyes drifted to Harold's nervously, "Not like I did."

"Did?" Harold repeated skeptically.

"I…you have no reason to believe me, I know that Harold," Claire swallowed hard, "After…I kidnapped you, I…I actually did start to question Samaritan," she shrugged. "And then I met Shaw."

Harold stared at her intently. "You've told me this story before, Ms. Mahoney. I'm afraid I see no reason to trust you now."

Claire nodded. "I can change that, I think," she moved towards the living room and Root stepped forward, clicking the safety off on her gun. Claire sighed. "Behind the couch. Your briefcase."

Root frowned but moved to the couch, pulling The Machine's custom briefcase from behind it. "What did you do to Her?" Root asked, turning to point her gun at Claire again.

"Nothing," Claire swore, "I…I've barely even looked at…Her."

Root cracked open the case, feeling relief wash over her as she heard the familiar whir of The Machine booting up. The Machine beeped to life, flashing a greeting across the screen and identifying Root as Her analogue interface.

"Did she hurt you?" Root asked, her voice tight. Whether she meant Claire or Shaw she wasn't entirely sure anymore.

The Machine beeped and then replied. _Negative._ The word flashed across the screen.

"Ok, what's going on?" Fusco said suddenly.

Opting to ignore Fusco, Root sighed in relief. "Why did Shaw bring us here?" she asked Claire. "Why would she steal The Machine and give it to a Samaritan agent?"

"That's…complicated," Claire said cautiously. "And…we don't have much time."

"Then talk quickly," Root hissed, gritting her teeth.

"I…began to question Samaritan's objectives after what you asked me Harold," Claire said shakily. "When you asked me if I thought Samaritan would shoot me to get you to cooperate I…I didn't want to believe it, but Greer he…" Claire shook her head. "I decided to keep looking and I…I found Shaw. Well, I found the recordings," her face darkened. "It was…horrible I…"

Root felt her stomach churn. She didn't want to know about Shaw's torture, not like this, not from her. Her hand tightened around her gun and she forced herself to breathe. Reese shifted, sensing her discomfort. "Move on," he ordered. Claire nodded.

"I couldn't do anything for her. I didn't…I didn't help," Claire admitted, hanging her head. "But I knew then, I knew that I was wrong. That Samaritan was dangerous, but I had no way out," she exhaled heavily. "It wasn't until later that I actually met Shaw. She was…not the first hostile agent Samaritan had turned, so I didn't think much of it… "

"When did they break her?" Reese asked suddenly.

"Why's that matter?" Root turned to him angrily.

"This could still be a trap. I want to know if they have their timeline straight," Reese muttered, barely blinking as he continued to stare at Claire.

Claire glared at him. "That's what I'm trying to tell you, they couldn't break her. They thought they did, but…Shaw was never…she fought. She fought everything."

"Doesn't look like it from here," Reese said icily.

"We were both assigned to Lambert for a time, working missions in the western half of the US. Eventually she approached me. Said she knew how I felt about Samaritan. That I wanted to stop it," Claire sighed. "I didn't believe her at first. It seemed like a trick, to test my loyalty. But later, on a mission to Istanbul, she saved my life. So when she asked me to come with her, while we were off duty there, I agreed."

Reese sighed. "Shaw mentioned working a mission in Wyoming," he offered tightly. Root nodded.

"Shaw took me to a Samaritan server farm, outside the city. She gave me a thumb drive and told me I had to go and install this inside the facility, in any server, just as long as I wasn't spotted. And I did. When I got back to Shaw, she had a laptop out and she gave it to me, to see if I could tell what I was looking at."

"And could you?" Harold tilted his head, his eyes narrowing as if he knew something.

"It was Samaritan's base code. It's DNA essentially. We couldn't see much, it would've known then, that we were watching, but it was like…staring into the Grand Canyon, it was vast and wonderful and terrifying," Claire's eyes lit up and Root glared at her. Claire sounded too much like her, like she used to be. Root shivered. She didn't want to think about the kind of person she would be if Samaritan had found her before she had found The Machine, before The Machine had opened her eyes and reminded her how to care about people.

"That sounds…familiar," Harold said slowly, looking at Root.

Root nodded. "It must have been the virus you wrote, the one you installed on Elizabeth Bridges computer." She turned to Claire. "How would Shaw know about that?"

"I…I don't know who you're talking about," Claire shrugged. "All I know is, Shaw told me to write a virus based on the code we had. It had to be fast acting and devastating. She said if I could write it, she could plant it," Claire inhaled deeply. "So I did. I built it. It took almost two months but it's done."

"You built a computer virus you believe capable of taking down an Artificial Superintelligence?" Harold asked skeptically.

"Based on the worm Shaw used, the one you wrote I guess, and the base code I saw, yes," Claire smiled proudly. "I made the virus invisible to Samaritan the same way your worm was, and after seeing the base code, how it was…written isn't a good enough word to describe…the elegance of…all of it," she bit her lip.

"Ok, let's not get too poetic about an ASI hell bent on world domination," Root drawled irritably.

"How could you possibly…" Harold shook his head, "How could you possibly think you could outsmart Samaritan with a virus?" the look he gave Claire sent a chill down Root's spine. It was how he used to look at her, before The Machine had saved her.

Claire sighed in frustration. "Every other Thursday at midnight Samaritan goes offline for 90 seconds. It scans itself for errors, updates itself, and reboots. And for those ninety seconds there's no one watching. Samaritan goes blind," she wrung her hands nervously. "And when the system comes back online, it rushes all that new data back to its server farms all over the world."

Root felt her mind racing. "If you installed the virus during that time, from the proper centralized location, when it wasn't watching-"

"Exactly!" Claire's shoulders sagged with relief, "Yes, exactly. If we uploaded the virus during that window, the virus would stay dormant, it'd be transmitted to every single server on Samaritan's network. And as soon as it was in every single server, it would activate, and Samaritan wouldn't have any defense because its entire system would be under attack concurrently. It's a scorched earth virus. We take everything at once and leave nothing."

"That…that could work," Root said quietly, turning to Harold, her eyes wide.

Harold nodded slowly. "It…it just might Ms. Groves," he agreed.

Claire shook her head. "It did work. Shaw installed it twenty minutes ago."

The air left Root's chest like she'd been punched. Sameen was alone, in the belly of the beast, with who knew how many Samaritan agents around her. The images began to fly through her mind, the smoke, bullets, a red button, that damn grate, and Shaw falling; falling to the ground at the stock exchange and off bridges. Her chest tightened and she struggled to breathe evenly as her vision blurred.

"Are the blackouts connected to this?" Reese questioned.

"Samaritan's power is fluctuating as it fights the virus," Claire confirmed. "It won't last long. Maybe forty more minutes…Then this is over," she smiled sadly.

Harold tilted his head. "If this is true, then you've done the impossible Ms. Mahoney. You should be much more…enthused…then you appear."

Claire's eyes watered, "I am happy, Harold," her lips quivered. "I'm grateful. Shaw gave me the chance to die doing the right thing."

Root froze. "What do you mean?" she asked quietly, forcing her voice to work.

"The implants," Claire brushed her hair to the side, showing them a four inch scar over her right ear. "They're networked to Samaritan. When Samaritan dies…it'll take all us with it. All of Samaritans active agents, those who understand what they're doing, who they're helping. Every asset, every agent…every murderer," her voice quivered. "Scorched earth and all."

Root shoved Claire against the wall before Root even realized what she was doing. Her fists were in Claire's shirt, lifting the girl off her feet with strength Root didn't know she possessed. "Turn it off," Root hissed, her vision blurring. "Right now."

Claire shook her head. "I can't." She looked nervously around the room. "And I wouldn't, even if I could."

Root's hands trembled and she jumped when Harold gently put his hand on her shoulder. "Hurting Claire isn't the answer Ms. Groves," he reminded her, his voice low and sympathetic.

Root released Claire, inhaling and exhaling deeply, gasping for breath. "Why Harold?...why would Sameen…" she stopped suddenly as a sob shook her body and she slumped against the wall, unable to stop the shivers that ran through her body.

The Machine beeped suddenly, and everyone turned to look at Her. _Sameen did this because I asked her to,_ the small black screen read.

* * *

 _Please stay safe. I'll be on tumblr and I know countless others will be too if you need to talk. -5/31/2016_


	17. Omission

_massive MASSIVE trigger warning for this chapter. this deals exclusively with Shaw's time in Samaritan, so torture and general shittiness from Greer, Martine, and Lambert are all over this chapter. Writing them makes my skin crawl tbh._

 _I wrote this months ago and now that we've seen so much of Shaws time with Samaritan on the show like...I honestly kinda wish this chapter didn't exist? So, if you wanna skip it please PLEASE do. The end notes of the chapter will have a summary and within like, 20 minutes of posting this I should have the next chapter up, so you can just skip right over this and keep reading. And on top of that trying to format this chapter was pure hell. So really, seriously, feel free to just pop on over to 18._

* * *

 _Operation_codename_Phoenix …Status…Initiate Step_01_

 **Cam_33/ 4th floor/ 20_Oct_14/ 1115 EDT**

Shaw's arms were tied over her head, her feet barely skimming the ground. There was blood pooled around her feet and she was screaming. Lambert stood in front of her. There was a blow torch at his feet.

 _~Primary Asset: Sameen_Shaw …Scream approaching 109 dB …Blood loss approx. 2.5 pints_ … _Conclusion: Class 2 hemorrhage, medical intervention advised_

"That'll be all," Greer ordered, stepping into the room.

Lambert nodded. "Of course." He turned to leave and paused at the door. "Should I clean up?"

"Concerned?"

Lambert grinned. "Only about your shoes. They're Bertuli's."

 _~Bertuli …Alessandro_Oxfords …Size_8 …$1,370.00 List Price_

"They'll survive Mr. Lambert," Greer smiled. Lambert left, closing the door behind him. Greer pulled a chair across the room and sat a few feet away from Shaw. "How're you doing today Sameen?"

Shaw glared at him, her nostrils flaring and her jaw tight. "Peachy," she hissed.

"Care to tell me why Samaritan is unable to see you or your friends?"

"Well, its what? Tuesday? So….no," Shaw drawled.

Greer raised an eyebrow. "It is a Tuesday as a matter of fact. That's quite impressive, given how long it's been since you've seen the sun," Greer responded. "It's October 20th to be precise. Almost Halloween."

Shaw swallowed hard, her breathing uneven, "I'm guessing I don't get to leave to go trick-or-treating," she muttered.

"Unfortunately not."

"Prolly smart," Shaw nodded, leaning forward against her restraints. "I could kill you with a tootsie roll."

Greer cocked his head, staring at her. "Are you always this unpleasant or do you reserve this hostility for me?" he asked coolly.

Shaw grinned. "Ask Lambert," her lip curled into a sneer.

Greer shifted forward. "Does being away from those you care about during the holidays bother you Sameen?"

Shaw glared at him. "I'm not that sentimental."

 _~Heart Rate Elevation Mild …Conclusion: Unease_

"I think it might," he said thoughtfully. "You don't just withstand…this," he gestured to the pool of blood at Shaw's feet, "For just anyone." He cocked his head again. "Not that they appreciate it. Your dedication."

Shaw rolled her eyes.

"They've left you here to rot. They aren't looking for you, they aren't coming," he said slowly, deliberately, watching Shaw's face closely for a reaction. "You are expendable to them."

"Good," Shaw hissed.

"Every time we have these little chats I regret more and more that I was unable to get to you first," Greer nodded thoughtfully. "Your skill, your tenacity…your pain tolerance. It's all very impressive Sameen. It's a shame your loyalty is so misplaced."

"I'll take your character assessment under advisement," Shaw muttered, her eyes fluttering closed.

 _~Conclusion: Exhaustion due to blood loss_

"Tell me how Ms. Groves communicates with The Machine," Greer ordered.

Shaw's eyes snapped open and she growled. "No thanks."

"Very well," Greer sighed. "I shall leave you in Mr. Lambert's capable hands then." Greer walked out, slamming the door behind him.

 _~Threat Anaylsis_Sameen Shaw_Day_56_

 _~Option 1-23,789 …Step 1: Alert Analogue Interface …Resulting Mortality Rate for Analogue Interface 98.4% +/- 0.002% error margin...Conclusion: Unable to alert Analogue Interface at this time_

 _~Option 23,790-47,892 …Step 1: Contact Primary Asset Sameen_Shaw …Chance of Discovery 23% …Mortality Risk to Primary Asset 43%...Conclusion: Inconclusive_

 _~Option 47,893-76,396 …Step 1: Maintain Silence …Mortality Risk to Primary Asset 97%...Conclusion: Intervention Necessary_

 _…Contacting Primary Asset…_

The lone light bulb in the room began to flicker, randomly at first, and then in code. _Can-You-Hear-Me?_

Shaw's shoulders tensed. Her breathing stopped.

 _~Heart Rate Elevation Significant …Conclusion: Contact established_

The light flickered randomly again, before repeating the code. _Can-You-Hear-Me?_

Shaw groaned as she shifted her shoulders, trying to look around the room. Her eyes settled on the camera and her jaw clenched. She looked away quickly and stayed completely still.

 _~Conclusion: Primary Asset Sameen_Shaw does not wish to talk_

 **Cam_33/ 4th floor/19_Jan_15/ 1530 EDT**

"Go to hell," Shaw hissed as Greer and Martine entered the room. Martine lingered by the door smirking. "Get her out," Shaw glared at Martine, thrashing forward against her restraints.

"That hurts Shaw," Martine smirked as she strode up to Shaw, raising a hand to her cheek, "And here I thought we were getting so close…Sweetie."

Shaw growled and launched forward, head butting Martine. Their heads connected with a crack, and Martine staggered back.

"Perhaps you've antagonized Sameen enough for now," Greer smiled.

Martine frowned as blood dripped from her nose, her eyes traveled back to Shaw who was still glaring at her.

Greer stared at Shaw intensely. "I warned you that your loyalty was misplaced," he said coolly.

Shaw stayed silent, her eyes on Martine.

"It was quick, if that helps," Greer offered. Shaw's eyes shifted to him. "Mostly, at least."

Shaw's breathing was ragged. "You got what you wanted," she said quietly. "Just get it over with."

"Why would we kill you when you've been so helpful?"

Shaw glared at him. "I didn't help you," she said slowly, her whole body shaking. "I was starved, drugged, tripped out on more hallucinogenic drugs than I can count-"

"You can't count to 12. Pity," Martine muttered, her voice muffled by her hand over her face.

"Does any of that really matter Sameen? Does it change the outcome?" Greer paused and then moved closer to Shaw. "Do you think that the technicalities of your betrayal mattered to Ms. Groves as she bled out?"

Shaw clenched her jaw, staring at Greer. "Get out," she whispered, her voice weak and small.

"I've come to offer you a way out," Greer strolled around the room, his hands in his coat pockets. "Come work with us. You are a talented soldier. Samaritan always needs more."

"No," Shaw growled.

"Thanks to the intelligence you provided there is no true opposition left," Greer smiled. "You already are Samaritan Miss Shaw."

"Maybe Martine can help you shove that offer up your ass," she hissed.

"You would rather waste away here, for no reason, for _no one_ , than come and work for Samaritan?" Greer shook his head, "That is quite disappointing. It's a waste of your talents."

Shaw remained silent and stared at the floor.

"Very well," Greer sighed. "You'll have an audience tomorrow then. Martine will be conducting a seminar, for the new recruits. The basics of information extraction," Greer's face darkened. "Samaritan can always find a purpose for you my dear Sameen." He left, slamming the door behind him.

Shaw was still for a long moment, and then slowly her index finger began to tap against her other arm. _Is-It-True?_

 _~Option 1-4,572 …Step 1: Truth/Primary Assets Participation in Operation_Phoenix 12% …Mortality rate of Analogue Interface 95%...Mortality Rate of Primary Asset John_Reese 87.4%...Mortality Rate of Admin Harold_Finch 99.8%...Mortality Rate of Primary Asset Sameen_Shaw 85%...Probability of total failure against Samaritan 99.99998%...Probability that Samaritan will allow humanity to survive 50%...Conclusion: Results unfavorable_

 _~Option 4,573-8,138…Step 1: Lie/Primary Assets Participation in Operation_Phoenix 85%...Mortality rate of Analogue Interface 45%...Mortality Rate of Primary Asset John_Reese 37.2%...Mortality Rate of Admin Harold_Finch 55%...Mortality Rate of Primary Asset Sameen_Shaw 98.998%...Probability of total failure against Samaritan 35%...Conclusion: Viable Option…Option Selected: 5,194_

 _…Contacting Primary Asset…_

 _I-Am-Sorry._

Shaw shuddered and rested her head against her forearm, shaking almost imperceptibly. She stilled a moment later, and resumed tapping her index finger to her forearm. _Make-Them-Pay._ There was a long pause. _Please._ She added.

 _You-Can-Help._

Shaw shifted slightly.

 _~Heart Rate Elevation Significant...Conclusion: Commitment_

The tapping began again. _How?_

 _Step-One-Locate-Elizabeth-Bridges._

 **Cam_44/ 4th floor/ 21_Jan_15/ 1600 EDT**

Greer stood in a hallway with Martine and Lambert.

"Well?" Martine asked, rising from her position leaning against the wall.

"Do not go easy on her tomorrow," Greer said. "Samaritan wants her in the field as soon as possible."

Martine grinned. "Of course."

"The voice synthesis is complete. We can contact her associates whenever you wish," Lambert said, holding up a tape recorder.

Greer smiled. "Let's hear it."

Lambert pushed a button. "Root-are you there? It's me. I need your help-" he stopped it.

"Impressive work," Greer nodded.

"Thank you sir."

"We won't be using it just yet," Greer added

"What? Why?" Martine frowned. "You already told her they were all dead, let's follow through."

"I haven't the faintest idea," Greer laughed. "But that is what Samaritan wishes. We will use this information when Samaritan knows it to be the right decision."

"Wish I'd known I was on such a lax deadline," Martine grumbled. "You really think we can turn her?" she added.

"Ms. Shaw is pragmatic. I imagine that her loyalty to her former comrades is more based on principle at this point than any actual feeling on the matter. Eventually, she will get bored of holding on to things that no longer exist," Greer shrugged, "Well, as far as she knows, anyways."

"Sounds charming," Lambert drawled. "And how do you control someone like that?"

"Once we demonstrate the power of the implant I think she'll be fairly agreeable," Greer responded. "However I doubt her demeanor will improve tremendously," he shrugged.

 **Cam_33/ 4th floor/ 03_Feb_15/ 1400 EDT**

 _Greer-Approaching._ The lights flickered.

Shaw stiffened, inhaling deeply. _Any-Last-Words?_ She tapped on her arm.

 _Knowledge-Of-Operation-Increases-That-Individuals-Mortality-By-98%-Conclusion-Tell-No-One._

Shaw bopped her head slightly in acknowledgement. Greer opened the door to the cell.

"Hello Sameen," he smiled. "Martine has certainly been busy, hasn't she?"

Shaw growled.

Greer raised an eyebrow. "Elegant," he said dryly.

"I'll do it," Shaw said weakly.

"Do what?" Greer asked, a smile tugging at his lips.

"If you let me work the numbers, like I did for ISA, I'll join you," Shaw grit her teeth. "Terrorist are still terrorist. No matter which robot wants to rule the world."

Greer smiled broadly. "I'm very glad to hear you've come around, even if your grasp on the technology in play is rather lacking," he turned towards the door. "Lambert," he called. Lambert entered the room. "Cut Ms. Shaw down and get her to the infirmary."

"Of course Sir," Lambert nodded, moving towards Shaw.

 _~Operation_codename_Phoenix…Status/Step One: Complete…Analogue_Interface_02: Activated_

* * *

 _Chapter Summary:In a chapter with truly horrific formatting... The Machine monitored Shaw the whole time she was in Samaritans custody, even as Greer hammers home Shaw's supposed 'expendability'. The Machine is in the electrical circuit and she uses that to make contact with Shaw and ends up letting Shaw believe Team Machine is dead in order to motivate Shaw to participate in 'operation phoenix' (aka her resurrection). Shaw gets hurt more. Its gross. I don't like it. But she does break Martines nose? So theres that._

Anyways...I know theres been a shitload of debate over how things played out yesterday. Just know that if you are hurting, it isn't silly or an overreaction and you're totally one zillion percent allowed to feel sad or angry or whatever. And if you need to talk to someone PLEASE do.

 _-6/01/2016_


	18. Consensus

_Reading this chapter I think it will be immediately apparent that I have never coded a damn thing in my life and, infact, can barely tell a computer from a paper weight. Have fun :)_

* * *

/Location: New York: Manhattan

40°45'46.4"N 73°58'43.9"W

0030 EDT

15 May 15/

"Turn it off," Root ordered, staring at The Machines small screen where security footage of Shaw in her cell was still playing. Root inhaled deeply, her whole world was spinning and she felt fury bubbling in her chest. "You knew. You knew the entire time," She bit out. "She was alive and …You were _watching_ … and you said nothing."

 _It-Was-Nessecary._ The words flashed across the small screen.

Root laughed hollowly. "You lied to her. You let her think we were dead so she'd do what you wanted," Root shook her head, pressing her palms against her eyes. Greer hadn't managed to break Shaw. The Machine had. Everything Shaw had done was at The Machines request. "Sameen is going to die for you," Root's voice broke, "Because of you. Because you asked her to do this."

 _She-Is-Saving-You._ The Machine said simply, as if that was an explanation or justification. _Saving-All-Of-Us._

Root reeled back as if she had been slapped. It's the most She has said to Root in months and the words cut through her. The room was still spinning and Root bit her lip hard to stop from crying. Shaw hadn't signed up for this, to serve Her. Root had. She had pledged herself, her blood, sweat, tears, her very life, to Her.

"Why," Root whispered. The Machine should have chosen her for this mission, not Shaw.

 _Clarification-Needed._

Root shook her head, her voice stuck in her throat. Her eyes drifted to Harold, expecting him to chime in with some variation of 'I told you so', but he just looked at her sadly.

He turned to The Machine. "You told me…" he shook his head slowly. "How could you justify this? Any of this? The loss of life you're causing…"

The screen blinked and switched to security footage. Shaw and Finch were walking through an office building full of election posters.

" _Any word from Root?" Shaw asked._

 _Finch didn't look at her as he answered. "It's going to be a long fight, but it must be won. At any cost," he sighed. Shaw froze._

The screen blinked again and an audio file began to play.

" _She taught me to value life, but war requires sacrifice."_

More files kept playing.

" _We will win this war" "If we do, there's no chance in hell all of us make it out alive. You have to be prepared for that."_

" _I don't need protection ok. I do the protecting."_

Root closed her eyes, feeling a wave of dizziness rush over her.

The screen blinked again and went black.

 _All-Other-Scenarios-End-In-Extinction-Via-Samaritan. This-Is-Essential-For-Survival._

Root tilted her head slightly, her stomach in knots. "For whose survival?" Finch asked slowly.

Claire fidgeted nervously. "I think this is…why Shaw brought me that briefcase."

Root froze and drew a ragged breathe.

"Why?" Harold asked.

"A week ago she called me and asked if we could reverse engineer an…antidote of sorts…" Claire laughed. "If I could write a cure for the virus I had just risked my life creating."

"Could you?" Root asked, her voice hollow, her fingers digging into her palms.

"Sort of," Claire said slowly. "You need to understand…we've been working on this for months. Right under Samaritan's nose. She'd never deviated from the plan she laid out. Not once. Not until a few days ago, when she got back to New York."

"When she realized we were alive," Root said, her voice cracking. Which was something She had to have anticipated?

"I guess," Claire shrugged. "When I talked to her about this cure, I realized what she wanted was more of a vaccine."

"A vaccine?" Harold's eye twitched briefly. "For what?"

"For your machine Harold," Claire smiled. "If we upload the vaccine into your machine, it'll be immune, and we can remotely hack Samaritan. It's too weak to fight us. And your machine will take over. It'll gain access to everything Samaritan is, everything it has."

Root blinked back tears, "She'd be safe?" her voice sounded hollow, even to her own ears.

Claire shook her head. "I don't know, this is all…new. I've barely looked at…Her," she gestured to the briefcase. "The virus, well, it's devastating Samaritans DNA, wiping out the rules that govern it, wiping the core of Samaritan away. But everything Samaritan has, its access, the cameras, its power… that could all be salvaged. By loading the machine onto Samaritans infrastructure you could save your machine, rebuild Her right now."

"She'd become responsible for the implants and stop them from triggering," Root clarified.

"Potentially," Claire said slowly, seemingly afraid to give Root or herself false hope.

Root nodded numbly and turned to Harold. "We have to do it Harold," she said quietly, her voice breaking.

Harold's eyes widened. "You realize Ms. Groves that this is exactly what The Machine wants. As a matter of fact, this is probably why The Machine chose Miss Shaw for this job," his voice was raising angrily, "The Machine knew you wouldn't let harm come to Ms. Shaw, and with this vaccine, if you let her, She'll gain access to all of Samaritan's resources." He glared down at the briefcase. "She is effectively holding Sameen and countless Samaritan agents hostage to get what she wants. More than ever I shudder to think what She would do with an open interface."

Root swallowed hard and shook her head. The Machine was still giving them a choice. They could let Samaritan die, taking its fanatics with it, and rebuild Her in peace using whatever precautions or specifications Harold wanted or they could rebuild her now, instantly, with more power and less safeguards than ever before. But She was still letting them make that decision. If these were the options than it was only because there were no viable alternatives. But She'd risked Shaw to do it. Shaw who had already sacrificed her life for the team and who had only just come back. And She'd lied to both of them to make it happen.

"I won't lose Shaw again," she glared at him. "Maybe you're right. This is the god you built Harry but-" she inhaled deeply against the lump in her throat, "I don't like how She chose to do things," she admitted, "But this is as close as we've gotten to taking out Samaritan. Maybe it was the only way."

 _I-Respect-Your-Choice. Whatever-It-May-Be._

Harold's lip curled. "Yes, I imagine you would now that you've strong armed us," he murmured.

Claire shifted uncomfortably. "If you want to use the vaccine we need to get going. It won't be long now until Samaritan is gone."

Blinking rapidly Harold spun around to Claire. "Remotely hacking Samaritan…we would have to be quite close for that to work, wouldn't we Ms. Mahoney?"

"Yes," Claire nodded. "Samaritan headquarters is right through that window," she gestured behind her, to the building across the street.

"When you said you built this under Samaritans nose you really weren't kidding," Reese raised an eyebrow, almost smiling.

Harold pursed his lips. "Perhaps…there is a third option," he said cautiously.

"We don't have time for a debate if we want to save Shaw," Root said, gritting her teeth.

Harold nodded and held up a hand to try and ease her. "We are mere feet away from Samaritan's brain Ms. Groves. I can't access that data remotely, but if I was on-sight…I could lock Samaritans existing infrastructure much like The Machine is currently."

Root frowned. "So, She'd be able to communicate-"

"But she would still rely on human agents for action, unlike Samaritan. There would be no rigged elections, no assassinations, no Maple," he nodded. "She would not retain the ability to interfere at that level," he paused, staring at her intently. "And I hope, after this, you can see why that might be for the best," he added, trying to be gentle.

She winced but nodded. Maybe this was the only way forward, but that She could be so reckless, could so casually throw away Sameen's life…she bit her lip. They could debate the morality of the choice later, once Shaw was safe. "Can you modify the code fast enough?" she asked.

He nodded crisply. "I believe so." He looked around the room nervously. "So we're in agreement? We're going into Samaritan's headquarters?"

Reese nodded.

"If there's a chance I don't have to die for this…I'll help however I can," Claire promised.

"I have no idea what any of you are talking about, but if you need me, I'm there," Fusco promised. Reese put a hand on his shoulder.

"You're already injured and you have a son Lionel," Reese said coolly.

Fusco glared at him. "I'm still a cop Wonderboy."

Reese smiled, "A good one, I know. But you need to sit this one out," he added, putting his hand on his partners shoulder.

Fusco glared at him silently before nodding once in resignation. "You get her out of there this time, you hear?"

"We won't leave her again," Reese promised, nodding to Root solemnly as he said it.

The Machine beeped frantically.

 _Odds-Of-Survival: Analogue-Interface-2.0002%_

 _Odds-Of-Survival: Admin-1.0009%_

 _Odds-Of-Survival: Primary_Asset-John_Reese-4.005%_

 _Odds-Of-Survival: Claire_Mahoney-1.000001%_

 _Odds-Of-Survival: Primary_Asset-Sameen_Shaw-0.0000000001%_

Root's eyes skimmed over the statistics, feeling her heart skip at Shaw's chances.

"Well," Harold said dryly, "At least we know."

"Better than my odds now," Claire added.

 _Option-Not-Viable._ The Machine whirred, sounding almost frantic.

"We can't wait any longer," Root said coldly.

"Agreed," Harold sighed.

"Good thing we stocked up before we got here," Reese added with a smirk, throwing the duffle bag he had brought in onto the counter. "Grab whatever you need," he said to Claire. She nodded nervously and pulled out a rifle and hand gun. She tucked the handgun into the waistband of her jeans.

Brazenly Claire led them through the hotel, not needing to avoid the cameras. On the street, the lights on the block were flickering on and off, sirens seemed to be sounding all around them, but all Root could hear was the blood pounding in her ears. Claire's access card got them into the lobby.

"Where to?" Reese asked.

"The servers are three floors down, the elevator is this way," Claire said. "This doesn't make sense…there should be more people…"she added nervously.

"There's nothing to protect here," Reese said quietly. "Everyone's three floors down."

"Or they know what will happen when Samaritan goes down," Root said coldly. "And they've gone to make peace. Call their loved ones," her voice tightened.

"Elevators over here," Claire said, rushing ahead of them and calling the elevator.

The elevator door opened with a ding and Root froze. The inside of the elevator was caked with blood, it was smeared on the walls and across the floor, the bodies of Samaritan agents littered the floor. Sitting in the middle of it was Shaw. Shaw was pale as a ghost, her eyes were barely open, and her breathing was loud and desperate. Despite that, she still managed to glare at them all furiously as her gun dropped to her side with a thunk.

"What. The hell. Are you nerds doing here," she hissed.

* * *

 _Two chapters left. So...I guess the fic will be finished Friday night. -6/01/2016_


	19. Ashes

_Sorry this didn't get posted last night, I had more editing notes for it than I originally remembered._

* * *

/Location: New York: Manhattan

40°45'44.5"N 73°58'45.4"W

0040 EDT

15 May 15/

Shaw's head lulled back against the side of the elevator and the gun slipped from her blood stained hands. Root was at her side in an instant, her hands on Shaw's face and stomach, her jeans stained red from the pool of blood she was left kneeling in.

"No, Sameen," Shaw's eyes flutter open, "Stay with me," Root's voice cracked.

Shaw stared at her for a moment before her eyes rolled past Root and focused on Claire. She stared at the younger girl murderously. "This wasn't the plan," Shaw hissed, the words half slurred. "You were supposed to keep them safe." Claire shook her head, her mouth hanging open, completely at a loss for words. The girl had probably never seen this much blood in her life. Root was sure she never had. Not while the person was still breathing.

"Any plan where you don't make it out of here doesn't work for me Sameen," Root argued, her eyes stinging as she fought back tears. Reese pulled his coat from his shoulders and handed it to her. Root stuffed it against Shaw's stomach and Shaw growled, too weak to protest. The blood was thick and everywhere and Root knew that even if they could save Shaw from this it would haunt her forever.

"That wasn't the mission," Shaw mumbled. Her eyes drooped shut before snapping back open.

"And what was? Burning Samaritan to the ground? Resurrecting The Machine?" Root shook her head, forcing down the lump in her throat.

"Both," Shaw's shoulder lifted in what Root thought was probably supposed to be a shrug.

"We need to get her out of here Ms. Groves," Finch added, stepping forward.

"Too late," Shaw sighed, her voice weak and her words slow from blood loss. Shaw dragged a bloody hand up to Roots shirt and pulled on the hem feebly. "Root, get out," she added feebly.

Root shook her head, feeling tears burn in her eyes. "No way. You're not doing this again," her voice cracked.

"This was the plan," Shaw slurred, her eyes lulling shut, "I had to fix this," she muttered.

"Fix what?" Root cupped Shaw's cheek, running her thumb back and forth, ignoring the blood that smeared across Shaw's too pale face. "Sameen?" her voice cracked again.

"I killed you," Shaw whispered, her eyes still closed.

"No, I'm right here sweetie," Root increased the pressure on the wound and turned to Reese. "Help me move her," she ordered, forcing her voice to be level.

Reese slid into the elevator to grab her and Shaw's eyes opened, "I told Martine Root," she said looking at Root with glassy eyes, half delirious. "I broke," she admitted in a whisper, her voice wavering, and Root felt her stomach drop. Reese scooped Shaw into his arms, and Shaw was too weak to even try and fight him off. She looked so tiny, so fragile.

"I'll get her out Root," Reese promised, before turning and practically sprinting out of the lobby with Shaw tucked against his chest.

Harold pulled Root to her feet, and Root knew he was talking to her but she couldn't hear a word of it. Shaw had done all of this because of her. She thought her 'betrayal' had cost Root and the others their lives and she'd lit the world on fire in response. She'd waged an almost singlehanded war with Samaritan to atone for it. Root felt ill. She'd blamed The Machine for what Shaw was doing, but the truth was Shaw only trusted The Machine because she had trusted Root first.

"She can't…Harold," Root turned to him, her eyes wide and desperate. "Please," she added, not sure what she wanted him to do.

"Ms. Shaw needs you to focus right now Root," Harold said, staring at her intently. "We don't have much time."

Root nodded and inhaled deeply. Even if Reese got her to a hospital, she'd be dead in minutes if they didn't stop Samaritan. Root wiped the blood off her palms as best she could and picked her guns up off the floor.

"Let's go," Root said coldly.

Claire blinked, clearly surprised by her sudden turn but Harold only nodded and stepped into the elevator.

"Three down you said?" He asked. Claire nodded.

They emerged from the elevator three floors down. The lights flickered on and off in the empty hallway.

"Looks like you were right," Claire said, her voice unsteady. "Most people went for their loved ones."

Root grit her teeth. "Samaritan has plenty of true believers," she assured the younger girl. "This place isn't empty."

"How do you know?" Claire asked, her voice small and childlike.

Root blinked. "Because destroying the belief of the faithful is not an easy task Ms. Mahoney," Harold said quietly. Root nodded and paused to stare at the collection of bodies on the ground. Shaw had been here.

"Where is this server room?" Root asked.

"This way," Claire said, running down the hall at full speed. Root jogged behind her, not wanting Claire to turn a corner into a wall of Samaritan agents but mindful of Harold's slower speed.

A team of heavily armed operatives charged through the doors at the end of the hallway. Root ducked behind a wall, relieved to see Harold had already done the same. The men screamed, yelling orders, and fired their assault rifles down the hall towards their position. Root took a deep breath and fired blindly around the corner. She heard one scream in pain and the sound of a body falling. Claire opened fire, giving her cover and Root popped her head from cover, kneecapping the rest of the team.

"We need to move," Root ordered as she reloaded. "The gunfire won't make us hard to find." She leaned down and pulled a radio from one of the men writhing on the floor. "This might come in handy," she added, kicking him across the face to knock him out. She tossed the radio to Claire.

Claire put the ear piece in her ear and nodded, before inspecting a growing spot of blood on her arm. "To the right," she jerked her head towards a set of large, red, double doors.

At the base of the door was a discarded security badge. Root grit her teeth. It's what Shaw had used. She held it up to the card reader and the doors slid open. She entered, her guns trained ahead of her in case they were walking into an ambush. Root sighed in relief; the room was empty.

The room was smaller than she expected, with a single computer in the center. Root stood guard, while Harold approached the computer, pecking away on the keyboard faster than she'd ever seen him type. He opened The Machine's case and connected it to the Samaritan computer.

Root bit her lip. This was their only option. They had to save Shaw, and letting The Machine have the sort of unrestrained power Samaritan had seemed completely out of the question now. Even before today Harold would never have allowed it. And now, Root wasn't so sure he was entirely wrong for believing that. But even this would have unintended consequences. She shook her head and inhaled deeply. Now wasn't the time to think about that. None of it mattered if they didn't make it out of here, if she didn't make it back to Shaw. Her chest constricted at the thought and she swallowed hard against the lump in her throat. She had to make it back in time. There was so much left unsaid. Shaw couldn't die thinking she'd ever betrayed Root, no matter what Samaritan had put her through.

"How's it coming Harry?" she tried to smirk at him, but her lip quivered.

"I need five more minutes Ms. Groves," he said brusquely.

"Reinforcements are here, you might have two," Claire yelled, just as bullets began to bounce around the room. Claire ducked behind a wall. "Or not," she shrugged, her eyes wide with fear.

Root and Claire stood on either side of the doors, taking turns firing down the corridor, creating a pile of agents in the middle of the hallway. The lights flickered again and Harold screamed.

Root whipped her head around in time to see Harold collapse to the ground.

"Go!" Claire screamed, firing down the hallway again to give her cover, while Root dragged Harold to the side of the room, a long red trail behind him.

"That was my own fault Ms. Groves," he said weakly, smiling at her as if he was embarrassed. "I…I was adding you, as…administrator," his voice waivered. The shooting outside had subsided, leaving only the groans and cries of wounded Samaritan soldiers drifting down the hallway.

"What?" Root shook her head, pressing her hands into the gunshot wound in his thigh; judging by the amount of blood it had hit his femoral artery. Without treatment he only had minutes, but she had no way to get him out.

"For a long time, I was fearful that you were too close to The Machine. That giving you that level of access, in addition to the special relationship you had with…Her, was dangerous. But…today, I realized I was mistaken. Your faith in her is not blind, or infallible," his lip trembled. Frantically, Root tore her jacket off and ripped the sleeve of her shirt off, tying it tightly around Harold's leg. He groaned in pain as she cinched it.

"We'll get you out of here Harold," Root promised.

Harold shook his head. "I'm afraid this was always going to happen someday Ms. Groves…Root." He smiled up at her fondly as tears poured down her cheeks, "I can think of no finer person to pass this responsibility…this burden…on to," he whispered. "You will keep her safe, but you will also keep the world safe from her," he nodded slowly. "I trust you with this…implicitly."

Root shook her head frantically. "Stop talking like that Harold, please. I can't lose you too," she plead.

Claire cocked her head to the side. "Reinforcements on the floor above us. We don't have much time."

He pursed his lips, fighting to stay conscious. "You aren't out of time yet. Go now. Ms. Shaw will need you," he said slowly, his voice pained. "I need…to finish the code…just a few more lines, I can instruct Ms. Mahoney."

Claire nodded, "I can do it," she promised.

Root shook her head. "I'm not leaving you," she argued.

Harold shook his head. "You have more to look forward to than death Ms. Groves. Wonderful things…" his lip trembled again and he raised his hand to her forearm, gripping it tightly. "Go," he ordered, staring at her intently.

"No one else will touch him Root," Claire stared at her, eyes wide and brimming with tears. Her jaw was jutted forward determinedly, her knuckles white on her gun. "I promise," she added, nodding her head.

Root nodded mutely, her head swimming. "I…Harold…" her voice cracked. What was there to say to him? A man who she had betrayed time and again, who had offered her not just his forgiveness but his friendship and trust, who had built the thing that had given her life meaning. He'd saved her, more times and in more ways than she could even count. "Thank you," she finished, staring at him through blurry eyes, desperately hoping it was enough.

He nodded once and smiled at her. "Go Root," he said quietly.

She stood and wiped her eyes, a small sob finally escaping her. Root pivoted quickly and sprinted back down the hallway, over the injured and dead Samaritan agents. Harold's voice was still in her ear. The comms crackled to life.

"Mr. Reese?" Finch asked, the pain evident in his voice.

"Finch?" Reese responded in concern. "Where are you?" he growled.

"Precisely where I need to be," Harold said, his voice steadier than it had been a minute ago.

Root kept running, tears trickling down her cheeks.

"Finch," Reese's voice cracked.

"It's ok, Mr. Reese," he soothed.

Root skidded to a stop, raising her guns in trembling hands. Jeremy Lambert trained his gun on her, glaring furiously. His clothes were tattered and singed and he was bleeding from a massive cut on his head.

"No, I'm almost to the hospital, I'll drop Shaw off, and I'll be back," Reese promised.

"It will be too late by then," he said sadly. In the background, Root could make out the sound of gunfire and Claire screaming.

"I do not have time for you right now," Root snarled. "Move."

"Can't do that lovely," Lambert sneered, stalking towards her slowly. "You've ruined it," his voice cracked oddly. "Samaritan could have made the world…so much better. Maybe even perfect," he shook his head. "How do you not understand that?"

"Just hang on Finch," Reese plead.

"I just…needed to tell you something Mr. Reese. You have, on more than one occasion, credited me with giving your life purpose again," Harold said, his voice low and tired. "And I need to say thank you before…before I am unable to do so, because you also gave my life purpose," Harold's voice waivered and a small whimper escaped his lips.

Root cringed. This wasn't for her to hear. She shouldn't be listening.

"Samaritan was never going to make the world better," Root shook her head at Lambert, her lips curling in disgust.

"Finch…" Reese's voice caught and he stopped.

"I should have known Sameen couldn't be turned," Lambert scoffed. "Greer was so sure he could control her," he shook his head.

The world seemed to fall away then and Root fired at Lambert, screaming. He dove behind cover as Root moved forward, still firing, refusing to give him an inch.

"Goodbye, Mr. Reese," Harold's voice trailed off.

Lambert fell to the ground, holding his knee, as blood pooled on the ground below him.

Root glared at him, her gun trained on him. He smiled up at her, bitterly. "Still knee-capping everyone I see," he chuckled and then grimaced in pain. Her hand trembled and she kept her finger off the trigger, afraid it would accidently fire. Lambert noticed and raised an eyebrow. "So you're not going to kill me," he smirked. "Suppose it doesn't change anything. I'll be dead soon enough," his eyes danced maliciously, "And so will she." Root pulled the trigger, almost smiling at the dull thud his body made as it hit the ground.

"Finch?" Reese called. "Finch?"

The line was dead.

Root threw up.

Blinking back tears, she resumed her sprint up the stairs, taking them two at a time until she was in the lobby. Tucking her guns into her waistband she sprinted down the block. It was almost one am, the streetlights, traffic lamps, and everything else flickered on and off. The cars on the street were paused, stalled in the confusion. Sirens bellowed in the distance and Root charged towards them. The hospital was just up the block. Her lungs burned as she gasped for air, and her stitches ripped open again, leaving a red trail down her side. Finally the ambulance entrance to the ER was in her sights and she surged forward.

She burst through the doors to utter chaos, a cacophony of screaming and crying around her. The lights flickered off then on again. Her eyes scanned the room quickly and she saw them. Reese with his head buried in his hands as two doctors worked frantically on Shaw, monitors beeped around her furiously.

There was still so much blood.

"You can't be here, Miss," a nurse said suddenly, dragging her towards the waiting room.

"No, that's my- that's Shaw, you can't-" Shaw's heartrate suddenly dropped off the monitor.

"She's coding," the doctor yelled, reaching for the paddles. He pressed them into her chest but the line didn't spike. Sound seemed to fade out of existence as Root pushed forward, fighting two nurses who were forcibly holding her back. She was screaming, she knew, but she couldn't hear it.

The lights flickered again and then held steady and a familiar hum started behind Roots right ear.

 _Can-You-Hear-Me?_

Root couldn't make her voice work to answer.

* * *

 _The next chapter is the end. And it WILL be up tomorrow.-6/03/2016_


	20. 2-point-O

_Wow. Ok. This is it. I just want to say thank you to everyone who has taken the time to comment or leave kudos on this. Knowing people have enjoyed this fic is just...really really awesome. I have...a lot of (often conflicting) feelings about whats going on with the show atm, but I'll always adore it for these characters and the amazing performances and relationship we got to see. When I initially wrote this I was afraid the ending would come off as too sappy, but uh...I'm pretty ok with it after this week haha. I hope that if this weeks episodes have you hurting that this helps even the tiniest of bits in giving you some peace or an alternate headcanon or whatever you need. And again, thank you so much for reading._

* * *

/Location: New York: Central Park

40°47'27.8"N 73°57'43.0"W

2115 EDT

21 May 15/

"No shoulder canon this time?" Control cocked her head, her eyes narrowing as she stared at Reese and Root.

Root offered a hollow smirk. "We only use those for special occasions," she reminded the older woman.

Control raised an eyebrow. "Well, I'm flattered," she said dryly.

"You can tell your men to stop pointing their guns at us now," Reese said quietly, his voice only mildly threatening.

Control held up her hand, waving off her guards. "You get two minutes," she growled, glaring pointedly at Root. "And that's only because of Shaw." Root flinched.

"How exactly did you get your job back so quickly?" Root pondered, her voice overly sweet.

Control's lip curled in distaste. "Officially, Samaritan is not and was never an enemy of the United States Government. No harm no foul," she shrugged.

"Bureaucracy is funny," Reese added lightly.

Control sighed. "Where is it?" she asked angrily. "That's why we're here, isn't it? You killed Greer and took Samaritan. And now, you think you can hold the United States Government hostage and name your price to sell it back to us."

A large grin spread slowly across Root's face. "No, that's, definitely not what's going on here," she smirked. She nodded once and Reese stepped forward, handing Control a manila file.

"What's this?" Control sighed, flipping it open.

"A new number," Root smiled.

"A number?" Control repeated slowly, starring at Root. "This isn't Samaritan."

Root ignored the question. "You stormed Samaritan's old headquarters and found an empty building. And you've been trying to track us all week, and frankly, we have our own injured to tend to. Plus we're sick of shooting your men," Root's smile stretched further across her face as Control's nostrils flared. "So I come bearing a message," Root blinked, listening intently to what She was saying, " _Stop looking for my agents. Stop looking for me. You will never be in control of me. But I value your purpose. Do your job. Stop hunting my people. I will continue to provide you with the numbers you need_ ," Root said evenly, blinking as the message stopped. She felt a chill run through her. Even now, when she couldn't help but question some of Her choices, speaking for Her was a rush that filled her with pride.

Control nodded slowly. "And if I choose to ignore your theatrical little warning?'

Root grinned. "Then the numbers stop and you become obsolete," she shrugged mischievously.

"You'd leave the country defenseless," Control growled, glaring at both of them.

Reese shrugged. "Just because you aren't getting the numbers doesn't mean no one is," he said simply.

Control nodded slowly, her jaw tight. "How do I get in touch with you?" she asked grudgingly.

"You don't," Root smiled.

"Root," Reese said suddenly, tapping his watch. "We have to go," he reminded her.

Root nodded and turned to Control. "This is your only warning. If you even think of pursuing us again, we will know, we will stop you, and I'll kill you myself." Control scowled at her. "Let's go John," she finished quietly.

/Location: New York: Cemetery

40°39'32.1"N 73°59'43.9"W

2200 EDT

21 May 15/

They stared down at the grave silently. Root gently placed her hand over Reese's, squeezing it. He blinked at her in surprise and she bit her lip.

"I'm so sorry John," she whispered, her voice raw.

Reese nodded slowly, his jaw tight. "Finch knew the odds Root. We all did," his voice cracked.

"I don't find that particularly comforting," Root admitted.

"No," Reese agreed darkly. He leaned down and put his hand over the grave, fingers tracing the name slowly. He nodded once and then abruptly stood up, his jaw tight.

"You don't have to leave," Root said quietly.

He blinked before turning to her, his lips thin. "I need a change of scenery," he said, his lip twitching into an almost smile.

She nodded. They strolled slowly back towards their cars, pausing at the top of the hill.

Claire was leaning against Reese's car, and she perked up instantly when she saw them.

"Are you sure about her?" Root asked, staring at the young woman skeptically. Her left arm was in a sling and she had stitches in her upper lip.

Reese smiled genuinely. "Finch always believed in second chances," he reminded her. He nodded his head slowly. "I think he'd want me to do this. He…had a soft spot for her." He sighed heavily. "Maybe I can give her some direction…a purpose," he added.

Root's throat tightened and she bit her lip, fighting back tears. "Harry would be proud," she said, her voice cracking. "Where will you two go?"

Reese shrugged, "Chicago." He pursed his lips. "Or maybe Miami. Somewhere with less polar vortexes," he grinned at her.

She nodded. "Wherever you set up, let me know, I can send you whatever you need," she promised. "You can work out your own system for getting the numbers, or…" she sighed in exasperation as commotion down the hill caught her attention; Shaw was yelling at Fusco as he tried to push her wheelchair up the hill. She shoved him off of her and hobbled to her feet. Fusco threw his hands up in exasperation and stalked away. Shaw stood unsteadily, one hand on Bear who stood loyally at her feet. Root's chest tightened. "What about Bear?" she asked quietly.

Reese frowned. "I think she needs him more," he nodded down the hill, watching Shaw smile as she rubbed the dog's ears contently. He shifted his gaze back to her. "She isn't ok Root," he said. Root jerked her head up and down once, unable to speak. "Shaw was alone in the dark for so long," he stared at Shaw sadly. "I'm not sure she remembers anything else," he turned to Root fully.

Root swallowed thickly, knowing Reese was right. She hadn't wanted to believe it, not until the hospital. She'd finally seen Shaw sleep then; with night terrors so intense she'd repeatedly ripped her stitches open from thrashing, waking so violently she'd broken a nurse's wrist. They'd started restraining her after that.

Since the Stock Exchange, they'd all been at war. But even Root had had her reprieve, moments of down time, however brief, when She would whisper in her ear that she was safe and could rest. Shaw hadn't had that, hadn't had a moment of security since the elevator. Shaw's body might have healed from what Samaritan did to her, and that was debatable in and of itself, but her mind certainly hadn't. Shaw hasn't been given that time. Not yet.

"She'll get there," Root said, her voice tight and determined.

"I hope so," Reese said, his voice small. "I…I need to do one more thing, before we go," he said suddenly. He put a hand on her shoulder briefly and then turned and left.

Root strolled back down the hill to Shaw. "You aren't supposed to be up," Root scolded half teasingly. Shaw glared back at her but didn't argue when Root practically shoved her back into the wheelchair. Her eyes drifted up and she saw Reese bent over another grave. "Whose is that?" Root asked quietly.

Shaw's eyes narrowed. "Carter's," she muttered, her voice tight. Root nodded somberly. "He's leaving isn't he?" Shaw said suddenly, turning to look at Root. "That's what you two have been muttering about all week," she added, pursing her lips in irritation, "When you think I'm unconscious."

"Most of the time you were unconscious Sweetie." Shaw rolled her eyes and Root grinned. "He's thinking Miami," she admitted.

Shaw huffed. "Wish we'd thought of that," she muttered.

"Oh?" Root asked, a large grin twisting across her face. That certainly had potential. Shaw in a bikini, drinks on the beach…along with other things on the beach…she shook her head. Now was probably not the time for that.

Shaw shrugged. "There are gonna be numbers anywhere. We might as well do all this somewhere there's actual sun."

Root's chest tightened and her stomach flipped. "So… _we…_ are saving numbers together?"

Shaw rolled her eyes. "What else would we do?" she asked, irritated. "Samaritan is gone. Its agents don't want to cross us because you and The Machine still control the implants. But the wars over," Shaw blinked and paused suddenly, her shoulders sagging slightly as if the weight of that statement finally hit her. "Haveta stay in New York now though," she added with a shrug. "Can't all leave Fusco," she muttered begrudgingly.

Root leaned forward against the wheelchair and lazily wrapped her arms around Shaw. Shaw stiffened reflexively before letting herself relax against Root slightly. "Is that really what you want Sameen?" Root bit her lip and stared down at Shaw anxiously.

Shaw leaned her head back against the chair and raised an eyebrow, staring up at Root. "Well, yeah," she said slowly. She tilted her head in confusion. "Is that…not…what you want?" she added, her brow furrowed as if she was trying to connect puzzle pieces that didn't quite fit.

Root smiled down at Shaw, "I want to be with you Sweetie," she said, tracing her hand along Shaw's jaw.

Shaw sighed and rolled her eyes, but there was a smile tugging at the very corners of her lips. "That's why I said we Root," she shrugged, as if it was the simplest thing in the world.

Root reached forward and pulled Shaw's hand into hers, planting a kiss next to a line of stitches in Shaw's wrist. Shaw shuddered slightly and Root smirked, glancing down at Shaw knowingly. They certainly had healing to do. But there was nowhere she would rather be, and Root knew without a doubt that Shaw felt the same. She beamed down at Shaw, "Then that sounds perfect."

* * *

 _Did I just create Person of Interest: Miami? Yes. Yes I did (CBS, look at me doing your job for you, you're welcome)._

 _Anyways._

 _I think the next fic I'm working on is going to be a season 3 of The 1OO fix-it/replacement fic that will be called "Love is Broken on the Battleground." But...after that...I have a notebook full of ideas for Person of Interest stuff, I just need to figure out if it'll work better as sequel to this fic or if I wanna twist it into a s5 fix it too. We'll see what happens._

 _Regardless of that, thank you again for sticking with this fic. And especially, thank you to broodystars, my beta, who helped me through this whole thing. -6/05/2016_


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